work/1_panel_design/20180706_blast_diptera.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Blast markers versus dipterian genomes: Anopheles gambiae, Aedes aegyptii, Culex pipiens, Drosophila melanogaster.\n",
    "\n",
    "Results:\n",
    "- 591 of 663 markers with unique location in agam genome left for analysis\n",
    "\n",
    "Minor results:\n",
    "- add unaligned species to metadata\n",
    "- reorder and rename columns"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Libraries and parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import pybedtools\n",
    "from Bio import AlignIO\n",
    "from Bio.Blast.Applications import NcbiblastnCommandline\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "DATA_DIR = \"../../../data/\"\n",
    "# blast db from Anopheles gambiae, Aedes segypti, Culex pipiens, Drosophila melanogaster genomes\n",
    "COMB_DB = DATA_DIR + 'genome/AgAaCpDm' \n",
    "# out\n",
    "AMPL_FILE = \"data/20180619_comb_ampl.maf\"\n",
    "META_FILE = \"data/20180619_comb_ampl_data.csv\"\n",
    "BLAST_FILE = \"data/20180706_blast_4sp.xml\"\n",
    "UPD_META_FILE = \"data/20180706_comb_ampl_data.xlsx\"\n",
    "UPD_AMPL_FILE = \"data/20180706_comb_ampl.maf\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## BLAST run"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">0\r\n",
      "CGTAACGGTAGAGGACGTTTCGTTGGTGTACCTGGTAGCGATAGAAAACCACTGGTACTATCAACATATCTCGATGCACAAGAACACCTGCCATACGCTGATGATTCCAACGCGGTAACGCCGATGTCGGAAGAAAATGGTGCAATCATCGTTCCAGTATACTATGCTAATTTAGGTACACTAT\r\n",
      ">1\r\n",
      "AGTGCTCCATTTTCGTTATTAAACACTAGCCTTCTTTGTCTGGAGTCTAACATTAAAGGTGGAATCACAGCATATGAGCGCATTTTCTTATCCTCCATGGCCTAAAAACATCGGAAGAATCGTATGAATAAACATTTTCATGGTTACCATTTAATACTATAAGATCCATTTGTTAACTTACCTGTTCTTGAAGACCATCCATGATCTCTTCAAGATCGGCTTCAGATTTTATTCTAGAACCTACACGATTAAATCGTTCCTTATCTTCCCGCTGCTTTCGAAGCTCC\r\n",
      ">2\r\n",
      "GCACACTGTGTCGTTAGCTTTAACCTTGAAACTTCTACCCTCCAGCAAGCGAGTGAGAGCGCCGCGAGAGTTGTGCCAGTACGCGGCTCCACCATGCGCCCGTTTCGGTCAGATCGTCGAAATCGCTTCCTAAAT\r\n",
      ">3\r\n",
      "GAGGATATAACGGCGAAAGTTTGGAGCATAAAGTCGGCGGATCAGTTGCAGTGCTTCCTACGACATATTGTGAAGGCGTTCACGGACAGCTATCCCCACGCGCGAATACCGGAGCGTTGGGCTCAGACTGCACTGCAGCTGGGGCTTAGCTGCTCGTCGCGCCACTATGCCGGGCGCAGTTTGCAAGTGTTCCGCTCGCTTAATGTACCAATCAATTCGCGCATGCTGT\r\n",
      ">4\r\n",
      "CGGATCCCATTTGGCTCGTTGTGATGCTGTTGAATGTTTTATCCTTTCCATTTGCTGTCGGCGTGCGAGCGATACTAGCAATACTCACAAGTAAACAGCATCAATCTTAATCACAGGTAATTAGGGTACATCAATTTTGCACTGAATTAATAGAGGTTTG\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "# extract agam sequences for markers removing alignment gaps\n",
    "# headers are 0-based numbers of markers\n",
    "agam_fa = 'data/temp_ampl.fasta'\n",
    "\n",
    "with open('data/temp_ampl.fasta', 'w') as o:\n",
    "    i = 0\n",
    "    ampl_seq = AlignIO.parse(AMPL_FILE, \"maf\")\n",
    "    for a in ampl_seq:\n",
    "        o.write(\">{}\\n\".format(i))\n",
    "        o.write(str(a[0].seq).replace('-',''))\n",
    "        o.write('\\n')\n",
    "        i += 1\n",
    "    \n",
    "!head {agam_fa}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on class NcbiblastnCommandline in module Bio.Blast.Applications:\n",
      "\n",
      "class NcbiblastnCommandline(_NcbiblastMain2SeqCommandline)\n",
      " |  Wrapper for the NCBI BLAST+ program blastn (for nucleotides).\n",
      " |  \n",
      " |  With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI\n",
      " |  replaced the old blastall tool with separate tools for each of the searches.\n",
      " |  This wrapper therefore replaces BlastallCommandline with option -p blastn.\n",
      " |  \n",
      " |  For example, to run a search against the \"nt\" nucleotide database using the\n",
      " |  FASTA nucleotide file \"m_code.fasta\" as the query, with an expectation value\n",
      " |  cut off of 0.001, saving the output to a file in XML format:\n",
      " |  \n",
      " |  >>> from Bio.Blast.Applications import NcbiblastnCommandline\n",
      " |  >>> cline = NcbiblastnCommandline(query=\"m_cold.fasta\", db=\"nt\", strand=\"plus\",\n",
      " |  ...                               evalue=0.001, out=\"m_cold.xml\", outfmt=5)\n",
      " |  >>> cline\n",
      " |  NcbiblastnCommandline(cmd='blastn', out='m_cold.xml', outfmt=5, query='m_cold.fasta', db='nt', evalue=0.001, strand='plus')\n",
      " |  >>> print(cline)\n",
      " |  blastn -out m_cold.xml -outfmt 5 -query m_cold.fasta -db nt -evalue 0.001 -strand plus\n",
      " |  \n",
      " |  You would typically run the command line with cline() or via the Python\n",
      " |  subprocess module, as described in the Biopython tutorial.\n",
      " |  \n",
      " |  Method resolution order:\n",
      " |      NcbiblastnCommandline\n",
      " |      _NcbiblastMain2SeqCommandline\n",
      " |      _Ncbiblast2SeqCommandline\n",
      " |      _NcbiblastCommandline\n",
      " |      _NcbibaseblastCommandline\n",
      " |      Bio.Application.AbstractCommandline\n",
      " |      builtins.object\n",
      " |  \n",
      " |  Methods defined here:\n",
      " |  \n",
      " |  __init__(self, cmd='blastn', **kwargs)\n",
      " |      Create a new instance of a command line wrapper object.\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Methods inherited from Bio.Application.AbstractCommandline:\n",
      " |  \n",
      " |  __call__(self, stdin=None, stdout=True, stderr=True, cwd=None, env=None)\n",
      " |      Execute command, wait for it to finish, return (stdout, stderr).\n",
      " |      \n",
      " |      Runs the command line tool and waits for it to finish. If it returns\n",
      " |      a non-zero error level, an exception is raised. Otherwise two strings\n",
      " |      are returned containing stdout and stderr.\n",
      " |      \n",
      " |      The optional stdin argument should be a string of data which will be\n",
      " |      passed to the tool as standard input.\n",
      " |      \n",
      " |      The optional stdout and stderr argument may be filenames (string),\n",
      " |      but otherwise are treated as a booleans, and control if the output\n",
      " |      should be captured as strings (True, default), or ignored by sending\n",
      " |      it to /dev/null to avoid wasting memory (False). If sent to a file\n",
      " |      or ignored, then empty string(s) are returned.\n",
      " |      \n",
      " |      The optional cwd argument is a string giving the working directory\n",
      " |      to run the command from. See Python's subprocess module documentation\n",
      " |      for more details.\n",
      " |      \n",
      " |      The optional env argument is a dictionary setting the environment\n",
      " |      variables to be used in the new process. By default the current\n",
      " |      process' environment variables are used. See Python's subprocess\n",
      " |      module documentation for more details.\n",
      " |      \n",
      " |      Default example usage::\n",
      " |      \n",
      " |          from Bio.Emboss.Applications import WaterCommandline\n",
      " |          water_cmd = WaterCommandline(gapopen=10, gapextend=0.5,\n",
      " |                                       stdout=True, auto=True,\n",
      " |                                       asequence=\"a.fasta\", bsequence=\"b.fasta\")\n",
      " |          print(\"About to run: %s\" % water_cmd)\n",
      " |          std_output, err_output = water_cmd()\n",
      " |      \n",
      " |      This functionality is similar to subprocess.check_output() added in\n",
      " |      Python 2.7. In general if you require more control over running the\n",
      " |      command, use subprocess directly.\n",
      " |      \n",
      " |      As of Biopython 1.56, when the program called returns a non-zero error\n",
      " |      level, a custom ApplicationError exception is raised. This includes\n",
      " |      any stdout and stderr strings captured as attributes of the exception\n",
      " |      object, since they may be useful for diagnosing what went wrong.\n",
      " |  \n",
      " |  __repr__(self)\n",
      " |      Return a representation of the command line object for debugging.\n",
      " |      \n",
      " |      e.g.\n",
      " |      \n",
      " |      >>> from Bio.Emboss.Applications import WaterCommandline\n",
      " |      >>> cline = WaterCommandline(gapopen=10, gapextend=0.5)\n",
      " |      >>> cline.asequence = \"asis:ACCCGGGCGCGGT\"\n",
      " |      >>> cline.bsequence = \"asis:ACCCGAGCGCGGT\"\n",
      " |      >>> cline.outfile = \"temp_water.txt\"\n",
      " |      >>> print(cline)\n",
      " |      water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5\n",
      " |      >>> cline\n",
      " |      WaterCommandline(cmd='water', outfile='temp_water.txt', asequence='asis:ACCCGGGCGCGGT', bsequence='asis:ACCCGAGCGCGGT', gapopen=10, gapextend=0.5)\n",
      " |  \n",
      " |  __setattr__(self, name, value)\n",
      " |      Set attribute name to value (PRIVATE).\n",
      " |      \n",
      " |      This code implements a workaround for a user interface issue.\n",
      " |      Without this __setattr__ attribute-based assignment of parameters\n",
      " |      will silently accept invalid parameters, leading to known instances\n",
      " |      of the user assuming that parameters for the application are set,\n",
      " |      when they are not.\n",
      " |      \n",
      " |      >>> from Bio.Emboss.Applications import WaterCommandline\n",
      " |      >>> cline = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True)\n",
      " |      >>> cline.asequence = \"a.fasta\"\n",
      " |      >>> cline.bsequence = \"b.fasta\"\n",
      " |      >>> cline.csequence = \"c.fasta\"\n",
      " |      Traceback (most recent call last):\n",
      " |      ...\n",
      " |      ValueError: Option name csequence was not found.\n",
      " |      >>> print(cline)\n",
      " |      water -stdout -asequence=a.fasta -bsequence=b.fasta -gapopen=10 -gapextend=0.5\n",
      " |      \n",
      " |      This workaround uses a whitelist of object attributes, and sets the\n",
      " |      object attribute list as normal, for these.  Other attributes are\n",
      " |      assumed to be parameters, and passed to the self.set_parameter method\n",
      " |      for validation and assignment.\n",
      " |  \n",
      " |  __str__(self)\n",
      " |      Make the commandline string with the currently set options.\n",
      " |      \n",
      " |      e.g.\n",
      " |      \n",
      " |      >>> from Bio.Emboss.Applications import WaterCommandline\n",
      " |      >>> cline = WaterCommandline(gapopen=10, gapextend=0.5)\n",
      " |      >>> cline.asequence = \"asis:ACCCGGGCGCGGT\"\n",
      " |      >>> cline.bsequence = \"asis:ACCCGAGCGCGGT\"\n",
      " |      >>> cline.outfile = \"temp_water.txt\"\n",
      " |      >>> print(cline)\n",
      " |      water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5\n",
      " |      >>> str(cline)\n",
      " |      'water -outfile=temp_water.txt -asequence=asis:ACCCGGGCGCGGT -bsequence=asis:ACCCGAGCGCGGT -gapopen=10 -gapextend=0.5'\n",
      " |  \n",
      " |  set_parameter(self, name, value=None)\n",
      " |      Set a commandline option for a program (OBSOLETE).\n",
      " |      \n",
      " |      Every parameter is available via a property and as a named\n",
      " |      keyword when creating the instance. Using either of these is\n",
      " |      preferred to this legacy set_parameter method which is now\n",
      " |      OBSOLETE, and likely to be DEPRECATED and later REMOVED in\n",
      " |      future releases.\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data descriptors inherited from Bio.Application.AbstractCommandline:\n",
      " |  \n",
      " |  __dict__\n",
      " |      dictionary for instance variables (if defined)\n",
      " |  \n",
      " |  __weakref__\n",
      " |      list of weak references to the object (if defined)\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data and other attributes inherited from Bio.Application.AbstractCommandline:\n",
      " |  \n",
      " |  parameters = None\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(NcbiblastnCommandline)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "blastn -out data/20180706_blast_4sp.xml -outfmt 5 -query data/temp_ampl.fasta -db /Users/am60/data/genome/AgAaCpDm -evalue 0.001\n"
     ]
    }
   ],
   "source": [
    "# generate blast command\n",
    "cline = NcbiblastnCommandline(cmd='blastn', out=BLAST_FILE, outfmt=5, query=agam_fa, \n",
    "                              db=COMB_DB, evalue=0.001)\n",
    "print(cline)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('', '')"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# run blast command. Return values are stdout and stderr\n",
    "cline()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## BLAST parse"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Score 151 (279 bits), expectation 1.9e-73, alignment length 184\n",
      "Query:       1 CGTAACGGTAGAGGACGTTTCGTTGGTGTACCTGGTAGCGATAGA...TAT 184\n",
      "               ||||||||||||||||||||||| || ||||||||||||||||||...|||\n",
      "Sbjct:  126707 CGTAACGGTAGAGGACGTTTCGTGGGCGTACCTGGTAGCGATAGA...TAT 126524\n",
      "173 184\n"
     ]
    }
   ],
   "source": [
    "# parse hits with NCBIXML\n",
    "# http://biopython.org/DIST/docs/tutorial/Tutorial.html#fig:blastrecord\n",
    "from Bio.Blast import NCBIXML\n",
    "blast_records = list(NCBIXML.parse(open(BLAST_FILE)))\n",
    "# http://biopython.org/DIST/docs/api/Bio.Blast.Record.HSP-class.html\n",
    "test_hsp = blast_records[0].alignments[1].hsps[0] \n",
    "print(str(test_hsp))\n",
    "print(test_hsp.identities, test_hsp.align_length)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'AaegL5_expect': '5.79208e-131;1.62185e-126',\n",
       "             'AaegL5_hits': 2,\n",
       "             'AaegL5_identity': '0.9196428571428571;0.9088235294117647',\n",
       "             'AaegL5_length': '336;340',\n",
       "             'AaegL5_q_span': '8-343;4-343',\n",
       "             'AaegL5_s_span': '3:25284012-25283677;2:45578367-45578028',\n",
       "             'AgamP3_expect': '6.98078e-180;3.43696e-138',\n",
       "             'AgamP3_hits': 2,\n",
       "             'AgamP3_identity': '1.0;0.9294117647058824',\n",
       "             'AgamP3_length': '343;340',\n",
       "             'AgamP3_q_span': '1-343;4-343',\n",
       "             'AgamP3_s_span': '2L:46338834-46339176;2R:39348407-39348746',\n",
       "             'BDGP6_expect': '1.65664e-111;1.00412e-103',\n",
       "             'BDGP6_hits': 2,\n",
       "             'BDGP6_identity': '0.8808139534883721;0.8716417910447761',\n",
       "             'BDGP6_length': '344;335',\n",
       "             'BDGP6_q_span': '1-343;8-342',\n",
       "             'BDGP6_s_span': '2R:11893567-11893910;3R:31740347-31740681',\n",
       "             'CpipJ2_expect': '2.05394e-140;5.79208e-131',\n",
       "             'CpipJ2_hits': 2,\n",
       "             'CpipJ2_identity': '0.9325513196480938;0.9196428571428571',\n",
       "             'CpipJ2_length': '341;336',\n",
       "             'CpipJ2_q_span': '3-343;8-343',\n",
       "             'CpipJ2_s_span': 'supercont3.222:571997-571657;supercont3.245:267778-268113'})"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# extract nececcary blast data\n",
    "from collections import defaultdict\n",
    "bd = dict()\n",
    "species = ('AgamP3', 'CpipJ2', 'AaegL5', 'BDGP6')\n",
    "for record in blast_records:\n",
    "    q = record.query\n",
    "    bd[q] = defaultdict(list)\n",
    "    for aln in record.alignments:\n",
    "        #extract species from hit definition\n",
    "        (s,c) = [l.split(':')[1:3] for l in aln.hit_def.split(' ') if len(l.split(':')) > 2][0]\n",
    "        if s not in species:\n",
    "            raise ValueError('Unknown genome ' + s)\n",
    "#         if s not in bd[q].keys():\n",
    "#             bd[q][s] = defaultdict(list)\n",
    "        for hsp in aln.hsps:\n",
    "            if (hsp.num_alignments is not None):\n",
    "                raise ValueError('Many alignmed fragments per HSP:\\n' + str(hsp))\n",
    "            bd[q][s + '_length'].append(hsp.align_length)\n",
    "            bd[q][s + '_identity'].append(hsp.identities / hsp.align_length)\n",
    "            bd[q][s + '_q_span'].append('{}-{}'.format(hsp.query_start, hsp.query_end))\n",
    "            bd[q][s + '_s_span'].append('{}:{}-{}'.format(c, hsp.sbjct_start, hsp.sbjct_end))\n",
    "            bd[q][s + '_expect'].append(hsp.expect)\n",
    "            i+=1\n",
    "        bd[q][s + '_hits'] = len(bd[q][s + '_length'])\n",
    "    for (k,v) in bd[q].items():\n",
    "        if type(bd[q][k]) is list:\n",
    "            bd[q][k] = ';'.join([str(s) for s in v])\n",
    "            \n",
    "bd['129']\n",
    "# example of duplicated marker"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'AaegL5_expect': '8.8269e-59',\n",
       "             'AaegL5_hits': 1,\n",
       "             'AaegL5_identity': '0.8268551236749117',\n",
       "             'AaegL5_length': '283',\n",
       "             'AaegL5_q_span': '4-286',\n",
       "             'AaegL5_s_span': '3:210133184-210132924',\n",
       "             'AgamP3_expect': '7.77149e-149',\n",
       "             'AgamP3_hits': 1,\n",
       "             'AgamP3_identity': '1.0',\n",
       "             'AgamP3_length': '287',\n",
       "             'AgamP3_q_span': '1-287',\n",
       "             'AgamP3_s_span': '2L:2926449-2926735',\n",
       "             'CpipJ2_expect': '2.43691e-64',\n",
       "             'CpipJ2_hits': 1,\n",
       "             'CpipJ2_identity': '0.8333333333333334',\n",
       "             'CpipJ2_length': '288',\n",
       "             'CpipJ2_q_span': '1-286',\n",
       "             'CpipJ2_s_span': 'supercont3.35:120152-120424'})"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# transform keys to int\n",
    "bd =  {int(k): v for k, v in bd.items()}\n",
    "bd[1]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Combine metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>aligned_len</th>\n",
       "      <th>aligned_species</th>\n",
       "      <th>chr</th>\n",
       "      <th>end</th>\n",
       "      <th>id_lineages</th>\n",
       "      <th>indels</th>\n",
       "      <th>informativeness</th>\n",
       "      <th>seqid</th>\n",
       "      <th>snvs</th>\n",
       "      <th>start</th>\n",
       "      <th>...</th>\n",
       "      <th>target_snvs</th>\n",
       "      <th>target_start</th>\n",
       "      <th>unid_species</th>\n",
       "      <th>exon</th>\n",
       "      <th>gene</th>\n",
       "      <th>intron</th>\n",
       "      <th>mRNA</th>\n",
       "      <th>repeat</th>\n",
       "      <th>utr</th>\n",
       "      <th>id lineage proportion</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>185</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>2403278</td>\n",
       "      <td>14</td>\n",
       "      <td>5</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>31</td>\n",
       "      <td>2403094</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>2403145</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>E013980A;E013980B;E013980C</td>\n",
       "      <td>AGAP004707</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004707-RA;AGAP004707-RB;AGAP004707-RC</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>345</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>2926735</td>\n",
       "      <td>18</td>\n",
       "      <td>96</td>\n",
       "      <td>0.857143</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>65</td>\n",
       "      <td>2926448</td>\n",
       "      <td>...</td>\n",
       "      <td>52</td>\n",
       "      <td>2926537</td>\n",
       "      <td>[{'AgamM1', 'AaraD1', 'AgamP3'}, {'AsteI2', 'A...</td>\n",
       "      <td>E014129A;E014130A</td>\n",
       "      <td>AGAP004734</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP004734-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.857143</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>199</td>\n",
       "      <td>17</td>\n",
       "      <td>2L</td>\n",
       "      <td>3249178</td>\n",
       "      <td>13</td>\n",
       "      <td>108</td>\n",
       "      <td>0.764706</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>19</td>\n",
       "      <td>3249043</td>\n",
       "      <td>...</td>\n",
       "      <td>13</td>\n",
       "      <td>3249077</td>\n",
       "      <td>[{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.764706</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>234</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>5026687</td>\n",
       "      <td>15</td>\n",
       "      <td>5</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>43</td>\n",
       "      <td>5026458</td>\n",
       "      <td>...</td>\n",
       "      <td>35</td>\n",
       "      <td>5026511</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...</td>\n",
       "      <td>E014976A</td>\n",
       "      <td>AGAP004892</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004892-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.714286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>321</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>5861628</td>\n",
       "      <td>15</td>\n",
       "      <td>191</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>10</td>\n",
       "      <td>5861468</td>\n",
       "      <td>...</td>\n",
       "      <td>8</td>\n",
       "      <td>5861515</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.714286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>156</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>6015616</td>\n",
       "      <td>13</td>\n",
       "      <td>5</td>\n",
       "      <td>0.619048</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>25</td>\n",
       "      <td>6015462</td>\n",
       "      <td>...</td>\n",
       "      <td>11</td>\n",
       "      <td>6015528</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>E015082A</td>\n",
       "      <td>AGAP004919</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004919-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>Yes</td>\n",
       "      <td>0.619048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>239</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>6045216</td>\n",
       "      <td>14</td>\n",
       "      <td>103</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>28</td>\n",
       "      <td>6045074</td>\n",
       "      <td>...</td>\n",
       "      <td>19</td>\n",
       "      <td>6045125</td>\n",
       "      <td>[{'AdirW1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>272</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>6091469</td>\n",
       "      <td>14</td>\n",
       "      <td>7</td>\n",
       "      <td>0.700000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>34</td>\n",
       "      <td>6091202</td>\n",
       "      <td>...</td>\n",
       "      <td>17</td>\n",
       "      <td>6091291</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...</td>\n",
       "      <td>E015094A</td>\n",
       "      <td>AGAP004923</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004923-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.700000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>163</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>6492034</td>\n",
       "      <td>13</td>\n",
       "      <td>40</td>\n",
       "      <td>0.684211</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>29</td>\n",
       "      <td>6491898</td>\n",
       "      <td>...</td>\n",
       "      <td>23</td>\n",
       "      <td>6491957</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.684211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>228</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>6534328</td>\n",
       "      <td>10</td>\n",
       "      <td>0</td>\n",
       "      <td>0.476190</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>32</td>\n",
       "      <td>6534100</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>6534177</td>\n",
       "      <td>[{'AfunF1', 'AdirW1', 'AmerM1', 'AgamP3', 'Ast...</td>\n",
       "      <td>E015172A;E015175B</td>\n",
       "      <td>AGAP004943</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004943-RA;AGAP004943-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.476190</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>193</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>6718015</td>\n",
       "      <td>12</td>\n",
       "      <td>59</td>\n",
       "      <td>0.631579</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>41</td>\n",
       "      <td>6717868</td>\n",
       "      <td>...</td>\n",
       "      <td>34</td>\n",
       "      <td>6717911</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.631579</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>153</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>6751068</td>\n",
       "      <td>10</td>\n",
       "      <td>19</td>\n",
       "      <td>0.476190</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>20</td>\n",
       "      <td>6750932</td>\n",
       "      <td>...</td>\n",
       "      <td>11</td>\n",
       "      <td>6750980</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AsteS1', 'Ast...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.476190</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>209</td>\n",
       "      <td>17</td>\n",
       "      <td>2L</td>\n",
       "      <td>6797100</td>\n",
       "      <td>16</td>\n",
       "      <td>96</td>\n",
       "      <td>0.941176</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>39</td>\n",
       "      <td>6796930</td>\n",
       "      <td>...</td>\n",
       "      <td>33</td>\n",
       "      <td>6796958</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.941176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>296</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>6963248</td>\n",
       "      <td>17</td>\n",
       "      <td>116</td>\n",
       "      <td>0.894737</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>50</td>\n",
       "      <td>6963036</td>\n",
       "      <td>...</td>\n",
       "      <td>44</td>\n",
       "      <td>6963081</td>\n",
       "      <td>[{'AquaS1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004950</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004950-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.894737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>296</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>6970020</td>\n",
       "      <td>18</td>\n",
       "      <td>116</td>\n",
       "      <td>0.947368</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>50</td>\n",
       "      <td>6969808</td>\n",
       "      <td>...</td>\n",
       "      <td>44</td>\n",
       "      <td>6969853</td>\n",
       "      <td>[{'AquaS1', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004950</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004950-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.947368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>244</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>6986625</td>\n",
       "      <td>13</td>\n",
       "      <td>4</td>\n",
       "      <td>0.619048</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>40</td>\n",
       "      <td>6986385</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>6986481</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>E015199A</td>\n",
       "      <td>AGAP004950</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP004950-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.619048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>202</td>\n",
       "      <td>17</td>\n",
       "      <td>2L</td>\n",
       "      <td>7248257</td>\n",
       "      <td>12</td>\n",
       "      <td>35</td>\n",
       "      <td>0.705882</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>21</td>\n",
       "      <td>7248079</td>\n",
       "      <td>...</td>\n",
       "      <td>13</td>\n",
       "      <td>7248156</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.705882</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>201</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>7666074</td>\n",
       "      <td>14</td>\n",
       "      <td>66</td>\n",
       "      <td>0.736842</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>34</td>\n",
       "      <td>7665920</td>\n",
       "      <td>...</td>\n",
       "      <td>25</td>\n",
       "      <td>7665983</td>\n",
       "      <td>[{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.736842</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>233</td>\n",
       "      <td>18</td>\n",
       "      <td>2L</td>\n",
       "      <td>7676953</td>\n",
       "      <td>13</td>\n",
       "      <td>105</td>\n",
       "      <td>0.722222</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>42</td>\n",
       "      <td>7676823</td>\n",
       "      <td>...</td>\n",
       "      <td>32</td>\n",
       "      <td>7676860</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.722222</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>280</td>\n",
       "      <td>18</td>\n",
       "      <td>2L</td>\n",
       "      <td>7715254</td>\n",
       "      <td>17</td>\n",
       "      <td>151</td>\n",
       "      <td>0.944444</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>46</td>\n",
       "      <td>7715076</td>\n",
       "      <td>...</td>\n",
       "      <td>36</td>\n",
       "      <td>7715116</td>\n",
       "      <td>[{'AaraD1', 'AgamP3'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.944444</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>247</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>7857099</td>\n",
       "      <td>15</td>\n",
       "      <td>112</td>\n",
       "      <td>0.789474</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>43</td>\n",
       "      <td>7856934</td>\n",
       "      <td>...</td>\n",
       "      <td>35</td>\n",
       "      <td>7856966</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AgamP3', 'AgamS1'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008-RA;AGAP005008-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.789474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>269</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>7857443</td>\n",
       "      <td>15</td>\n",
       "      <td>114</td>\n",
       "      <td>0.789474</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>54</td>\n",
       "      <td>7857227</td>\n",
       "      <td>...</td>\n",
       "      <td>45</td>\n",
       "      <td>7857272</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AaraD1', 'AgamP3'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008-RA;AGAP005008-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.789474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>244</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>7886168</td>\n",
       "      <td>16</td>\n",
       "      <td>75</td>\n",
       "      <td>0.800000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>36</td>\n",
       "      <td>7885974</td>\n",
       "      <td>...</td>\n",
       "      <td>27</td>\n",
       "      <td>7886034</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AmelC1', 'AgamS1'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005008-RA;AGAP005008-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.800000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>199</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>8146269</td>\n",
       "      <td>14</td>\n",
       "      <td>64</td>\n",
       "      <td>0.736842</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>35</td>\n",
       "      <td>8146115</td>\n",
       "      <td>...</td>\n",
       "      <td>28</td>\n",
       "      <td>8146154</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.736842</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>173</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>8226706</td>\n",
       "      <td>11</td>\n",
       "      <td>28</td>\n",
       "      <td>0.550000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>26</td>\n",
       "      <td>8226557</td>\n",
       "      <td>...</td>\n",
       "      <td>18</td>\n",
       "      <td>8226616</td>\n",
       "      <td>[{'AchrA1', 'AmerM1', 'AgamP3', 'AepiE1', 'Aar...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.550000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>321</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>8237283</td>\n",
       "      <td>15</td>\n",
       "      <td>102</td>\n",
       "      <td>0.789474</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>49</td>\n",
       "      <td>8237055</td>\n",
       "      <td>...</td>\n",
       "      <td>40</td>\n",
       "      <td>8237124</td>\n",
       "      <td>[{'AaraD1', 'AgamP3', 'AgamS1'}, {'AmelC1', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.789474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>314</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>8774650</td>\n",
       "      <td>14</td>\n",
       "      <td>9</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>53</td>\n",
       "      <td>8774345</td>\n",
       "      <td>...</td>\n",
       "      <td>40</td>\n",
       "      <td>8774409</td>\n",
       "      <td>[{'AchrA1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>E015672A;E015672B</td>\n",
       "      <td>AGAP005043</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP005043-RA;AGAP005043-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>158</td>\n",
       "      <td>15</td>\n",
       "      <td>2L</td>\n",
       "      <td>9310997</td>\n",
       "      <td>12</td>\n",
       "      <td>41</td>\n",
       "      <td>0.800000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>24</td>\n",
       "      <td>9310873</td>\n",
       "      <td>...</td>\n",
       "      <td>20</td>\n",
       "      <td>9310913</td>\n",
       "      <td>[{'AgamM1', 'AmerM1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.800000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>205</td>\n",
       "      <td>16</td>\n",
       "      <td>2L</td>\n",
       "      <td>9350411</td>\n",
       "      <td>11</td>\n",
       "      <td>38</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>30</td>\n",
       "      <td>9350228</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>9350274</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.687500</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>265</td>\n",
       "      <td>19</td>\n",
       "      <td>2L</td>\n",
       "      <td>9458250</td>\n",
       "      <td>16</td>\n",
       "      <td>153</td>\n",
       "      <td>0.842105</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>38</td>\n",
       "      <td>9458076</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>9458114</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AaraD1', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.842105</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>633</th>\n",
       "      <td>207</td>\n",
       "      <td>15</td>\n",
       "      <td>X</td>\n",
       "      <td>1144370</td>\n",
       "      <td>11</td>\n",
       "      <td>81</td>\n",
       "      <td>0.733333</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>27</td>\n",
       "      <td>1144219</td>\n",
       "      <td>...</td>\n",
       "      <td>20</td>\n",
       "      <td>1144261</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}, {'AquaS1', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.733333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>634</th>\n",
       "      <td>192</td>\n",
       "      <td>18</td>\n",
       "      <td>X</td>\n",
       "      <td>1816086</td>\n",
       "      <td>12</td>\n",
       "      <td>5</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>28</td>\n",
       "      <td>1815894</td>\n",
       "      <td>...</td>\n",
       "      <td>15</td>\n",
       "      <td>1815984</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...</td>\n",
       "      <td>E000519B;E000519A</td>\n",
       "      <td>AGAP000112;AGAP000113</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000112-RA;AGAP000113-RB;AGAP000113-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>635</th>\n",
       "      <td>234</td>\n",
       "      <td>15</td>\n",
       "      <td>X</td>\n",
       "      <td>4194191</td>\n",
       "      <td>13</td>\n",
       "      <td>127</td>\n",
       "      <td>0.866667</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>20</td>\n",
       "      <td>4194041</td>\n",
       "      <td>...</td>\n",
       "      <td>12</td>\n",
       "      <td>4194088</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000225</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000225-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.866667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>636</th>\n",
       "      <td>211</td>\n",
       "      <td>14</td>\n",
       "      <td>X</td>\n",
       "      <td>4692460</td>\n",
       "      <td>13</td>\n",
       "      <td>118</td>\n",
       "      <td>0.928571</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>13</td>\n",
       "      <td>4692320</td>\n",
       "      <td>...</td>\n",
       "      <td>4</td>\n",
       "      <td>4692359</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.928571</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>637</th>\n",
       "      <td>225</td>\n",
       "      <td>20</td>\n",
       "      <td>X</td>\n",
       "      <td>10000346</td>\n",
       "      <td>14</td>\n",
       "      <td>0</td>\n",
       "      <td>0.700000</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>32</td>\n",
       "      <td>10000121</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>10000169</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AgamS1'}, {'AaraD1', 'A...</td>\n",
       "      <td>E002410A;E002410C;E054460B</td>\n",
       "      <td>AGAP000562</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000562-RA;AGAP000562-RC;AGAP000562-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.700000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>638</th>\n",
       "      <td>283</td>\n",
       "      <td>15</td>\n",
       "      <td>X</td>\n",
       "      <td>11953530</td>\n",
       "      <td>13</td>\n",
       "      <td>133</td>\n",
       "      <td>0.866667</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>58</td>\n",
       "      <td>11953310</td>\n",
       "      <td>...</td>\n",
       "      <td>49</td>\n",
       "      <td>11953359</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.866667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>639</th>\n",
       "      <td>257</td>\n",
       "      <td>14</td>\n",
       "      <td>X</td>\n",
       "      <td>13339031</td>\n",
       "      <td>13</td>\n",
       "      <td>109</td>\n",
       "      <td>0.928571</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>41</td>\n",
       "      <td>13338825</td>\n",
       "      <td>...</td>\n",
       "      <td>32</td>\n",
       "      <td>13338883</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.928571</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>640</th>\n",
       "      <td>252</td>\n",
       "      <td>14</td>\n",
       "      <td>X</td>\n",
       "      <td>15480066</td>\n",
       "      <td>11</td>\n",
       "      <td>114</td>\n",
       "      <td>0.785714</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>34</td>\n",
       "      <td>15479861</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>15479905</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}, {'AsteI2', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.785714</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>641</th>\n",
       "      <td>278</td>\n",
       "      <td>12</td>\n",
       "      <td>X</td>\n",
       "      <td>18453487</td>\n",
       "      <td>10</td>\n",
       "      <td>128</td>\n",
       "      <td>0.833333</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>46</td>\n",
       "      <td>18453261</td>\n",
       "      <td>...</td>\n",
       "      <td>37</td>\n",
       "      <td>18453308</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000962</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000962-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.833333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>642</th>\n",
       "      <td>276</td>\n",
       "      <td>20</td>\n",
       "      <td>X</td>\n",
       "      <td>18742401</td>\n",
       "      <td>15</td>\n",
       "      <td>24</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>47</td>\n",
       "      <td>18742149</td>\n",
       "      <td>...</td>\n",
       "      <td>30</td>\n",
       "      <td>18742234</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}, {'AquaS1', 'A...</td>\n",
       "      <td>E003998A</td>\n",
       "      <td>AGAP000974</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000974-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.750000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>643</th>\n",
       "      <td>171</td>\n",
       "      <td>19</td>\n",
       "      <td>X</td>\n",
       "      <td>18759871</td>\n",
       "      <td>11</td>\n",
       "      <td>0</td>\n",
       "      <td>0.578947</td>\n",
       "      <td>AgamP3.chrX</td>\n",
       "      <td>31</td>\n",
       "      <td>18759700</td>\n",
       "      <td>...</td>\n",
       "      <td>19</td>\n",
       "      <td>18759759</td>\n",
       "      <td>[{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>E004008A</td>\n",
       "      <td>AGAP000974</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP000974-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.578947</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>644</th>\n",
       "      <td>192</td>\n",
       "      <td>17</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>1097727</td>\n",
       "      <td>13</td>\n",
       "      <td>61</td>\n",
       "      <td>0.764706</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>41</td>\n",
       "      <td>1097580</td>\n",
       "      <td>...</td>\n",
       "      <td>33</td>\n",
       "      <td>1097618</td>\n",
       "      <td>[{'AquaS1', 'AmelC1', 'AgamP3', 'AgamS1'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.764706</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>645</th>\n",
       "      <td>244</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>1181692</td>\n",
       "      <td>15</td>\n",
       "      <td>111</td>\n",
       "      <td>0.789474</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>29</td>\n",
       "      <td>1181534</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>1181591</td>\n",
       "      <td>[{'AgamM1', 'AaraD1', 'AgamP3', 'AgamS1'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.789474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>646</th>\n",
       "      <td>266</td>\n",
       "      <td>17</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>10022520</td>\n",
       "      <td>14</td>\n",
       "      <td>122</td>\n",
       "      <td>0.823529</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>40</td>\n",
       "      <td>10022361</td>\n",
       "      <td>...</td>\n",
       "      <td>31</td>\n",
       "      <td>10022415</td>\n",
       "      <td>[{'AgamM1', 'AmerM1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.823529</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>647</th>\n",
       "      <td>273</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>14190475</td>\n",
       "      <td>12</td>\n",
       "      <td>1</td>\n",
       "      <td>0.631579</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>41</td>\n",
       "      <td>14190202</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>14190278</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E012883A</td>\n",
       "      <td>AGAP012545</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP012545-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.631579</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648</th>\n",
       "      <td>328</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>14190530</td>\n",
       "      <td>13</td>\n",
       "      <td>1</td>\n",
       "      <td>0.684211</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>49</td>\n",
       "      <td>14190202</td>\n",
       "      <td>...</td>\n",
       "      <td>36</td>\n",
       "      <td>14190278</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E012883A</td>\n",
       "      <td>AGAP012545</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP012545-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.684211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>649</th>\n",
       "      <td>183</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>14190475</td>\n",
       "      <td>11</td>\n",
       "      <td>0</td>\n",
       "      <td>0.578947</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>30</td>\n",
       "      <td>14190292</td>\n",
       "      <td>...</td>\n",
       "      <td>14</td>\n",
       "      <td>14190351</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E012883A</td>\n",
       "      <td>AGAP012545</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP012545-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.578947</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>650</th>\n",
       "      <td>238</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>14190530</td>\n",
       "      <td>13</td>\n",
       "      <td>0</td>\n",
       "      <td>0.684211</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>38</td>\n",
       "      <td>14190292</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>14190351</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E012883A</td>\n",
       "      <td>AGAP012545</td>\n",
       "      <td>None</td>\n",
       "      <td>AGAP012545-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.684211</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>651</th>\n",
       "      <td>273</td>\n",
       "      <td>17</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>17273125</td>\n",
       "      <td>15</td>\n",
       "      <td>91</td>\n",
       "      <td>0.882353</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>56</td>\n",
       "      <td>17272921</td>\n",
       "      <td>...</td>\n",
       "      <td>43</td>\n",
       "      <td>17272987</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.882353</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>652</th>\n",
       "      <td>283</td>\n",
       "      <td>13</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>17913656</td>\n",
       "      <td>11</td>\n",
       "      <td>161</td>\n",
       "      <td>0.846154</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>26</td>\n",
       "      <td>17913483</td>\n",
       "      <td>...</td>\n",
       "      <td>20</td>\n",
       "      <td>17913523</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.846154</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>653</th>\n",
       "      <td>298</td>\n",
       "      <td>17</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>21709405</td>\n",
       "      <td>17</td>\n",
       "      <td>138</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>58</td>\n",
       "      <td>21709170</td>\n",
       "      <td>...</td>\n",
       "      <td>54</td>\n",
       "      <td>21709207</td>\n",
       "      <td>[]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>654</th>\n",
       "      <td>192</td>\n",
       "      <td>21</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>22100228</td>\n",
       "      <td>14</td>\n",
       "      <td>0</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>27</td>\n",
       "      <td>22100036</td>\n",
       "      <td>...</td>\n",
       "      <td>13</td>\n",
       "      <td>22100120</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>655</th>\n",
       "      <td>301</td>\n",
       "      <td>14</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>24502460</td>\n",
       "      <td>13</td>\n",
       "      <td>146</td>\n",
       "      <td>0.928571</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>31</td>\n",
       "      <td>24502215</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>24502303</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.928571</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>656</th>\n",
       "      <td>253</td>\n",
       "      <td>20</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>30650698</td>\n",
       "      <td>17</td>\n",
       "      <td>118</td>\n",
       "      <td>0.850000</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>41</td>\n",
       "      <td>30650492</td>\n",
       "      <td>...</td>\n",
       "      <td>33</td>\n",
       "      <td>30650530</td>\n",
       "      <td>[{'AquaS1', 'AgamP3', 'AgamS1'}, {'AsteI2', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.850000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>657</th>\n",
       "      <td>194</td>\n",
       "      <td>21</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>31108154</td>\n",
       "      <td>15</td>\n",
       "      <td>0</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>40</td>\n",
       "      <td>31107960</td>\n",
       "      <td>...</td>\n",
       "      <td>27</td>\n",
       "      <td>31108001</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.714286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>658</th>\n",
       "      <td>286</td>\n",
       "      <td>21</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>31857759</td>\n",
       "      <td>17</td>\n",
       "      <td>6</td>\n",
       "      <td>0.809524</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>43</td>\n",
       "      <td>31857478</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>31857533</td>\n",
       "      <td>[{'AquaS1', 'AmelC1', 'AgamP3'}, {'AgamM1', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.809524</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>659</th>\n",
       "      <td>254</td>\n",
       "      <td>21</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>31857857</td>\n",
       "      <td>15</td>\n",
       "      <td>76</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>23</td>\n",
       "      <td>31857641</td>\n",
       "      <td>...</td>\n",
       "      <td>5</td>\n",
       "      <td>31857754</td>\n",
       "      <td>[{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.714286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>660</th>\n",
       "      <td>200</td>\n",
       "      <td>19</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>31943559</td>\n",
       "      <td>17</td>\n",
       "      <td>99</td>\n",
       "      <td>0.894737</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>18</td>\n",
       "      <td>31943410</td>\n",
       "      <td>...</td>\n",
       "      <td>16</td>\n",
       "      <td>31943447</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.894737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>661</th>\n",
       "      <td>217</td>\n",
       "      <td>17</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>33274168</td>\n",
       "      <td>13</td>\n",
       "      <td>117</td>\n",
       "      <td>0.764706</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>14</td>\n",
       "      <td>33274010</td>\n",
       "      <td>...</td>\n",
       "      <td>11</td>\n",
       "      <td>33274053</td>\n",
       "      <td>[{'AgamM1', 'AmelC1', 'AaraD1', 'AgamS1'}, {'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.764706</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>662</th>\n",
       "      <td>279</td>\n",
       "      <td>13</td>\n",
       "      <td>UNKN</td>\n",
       "      <td>38751330</td>\n",
       "      <td>10</td>\n",
       "      <td>153</td>\n",
       "      <td>0.769231</td>\n",
       "      <td>AgamP3.chrUNKN</td>\n",
       "      <td>30</td>\n",
       "      <td>38751128</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>38751177</td>\n",
       "      <td>[{'AgamM1', 'AaraD1', 'AgamS1'}, {'AsteI2', 'A...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.769231</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>663 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     aligned_len  aligned_species   chr       end  id_lineages  indels  \\\n",
       "0            185               21    2L   2403278           14       5   \n",
       "1            345               21    2L   2926735           18      96   \n",
       "2            199               17    2L   3249178           13     108   \n",
       "3            234               21    2L   5026687           15       5   \n",
       "4            321               21    2L   5861628           15     191   \n",
       "5            156               21    2L   6015616           13       5   \n",
       "6            239               21    2L   6045216           14     103   \n",
       "7            272               20    2L   6091469           14       7   \n",
       "8            163               19    2L   6492034           13      40   \n",
       "9            228               21    2L   6534328           10       0   \n",
       "10           193               19    2L   6718015           12      59   \n",
       "11           153               21    2L   6751068           10      19   \n",
       "12           209               17    2L   6797100           16      96   \n",
       "13           296               19    2L   6963248           17     116   \n",
       "14           296               19    2L   6970020           18     116   \n",
       "15           244               21    2L   6986625           13       4   \n",
       "16           202               17    2L   7248257           12      35   \n",
       "17           201               19    2L   7666074           14      66   \n",
       "18           233               18    2L   7676953           13     105   \n",
       "19           280               18    2L   7715254           17     151   \n",
       "20           247               19    2L   7857099           15     112   \n",
       "21           269               19    2L   7857443           15     114   \n",
       "22           244               20    2L   7886168           16      75   \n",
       "23           199               19    2L   8146269           14      64   \n",
       "24           173               20    2L   8226706           11      28   \n",
       "25           321               19    2L   8237283           15     102   \n",
       "26           314               21    2L   8774650           14       9   \n",
       "27           158               15    2L   9310997           12      41   \n",
       "28           205               16    2L   9350411           11      38   \n",
       "29           265               19    2L   9458250           16     153   \n",
       "..           ...              ...   ...       ...          ...     ...   \n",
       "633          207               15     X   1144370           11      81   \n",
       "634          192               18     X   1816086           12       5   \n",
       "635          234               15     X   4194191           13     127   \n",
       "636          211               14     X   4692460           13     118   \n",
       "637          225               20     X  10000346           14       0   \n",
       "638          283               15     X  11953530           13     133   \n",
       "639          257               14     X  13339031           13     109   \n",
       "640          252               14     X  15480066           11     114   \n",
       "641          278               12     X  18453487           10     128   \n",
       "642          276               20     X  18742401           15      24   \n",
       "643          171               19     X  18759871           11       0   \n",
       "644          192               17  UNKN   1097727           13      61   \n",
       "645          244               19  UNKN   1181692           15     111   \n",
       "646          266               17  UNKN  10022520           14     122   \n",
       "647          273               19  UNKN  14190475           12       1   \n",
       "648          328               19  UNKN  14190530           13       1   \n",
       "649          183               19  UNKN  14190475           11       0   \n",
       "650          238               19  UNKN  14190530           13       0   \n",
       "651          273               17  UNKN  17273125           15      91   \n",
       "652          283               13  UNKN  17913656           11     161   \n",
       "653          298               17  UNKN  21709405           17     138   \n",
       "654          192               21  UNKN  22100228           14       0   \n",
       "655          301               14  UNKN  24502460           13     146   \n",
       "656          253               20  UNKN  30650698           17     118   \n",
       "657          194               21  UNKN  31108154           15       0   \n",
       "658          286               21  UNKN  31857759           17       6   \n",
       "659          254               21  UNKN  31857857           15      76   \n",
       "660          200               19  UNKN  31943559           17      99   \n",
       "661          217               17  UNKN  33274168           13     117   \n",
       "662          279               13  UNKN  38751330           10     153   \n",
       "\n",
       "     informativeness           seqid  snvs     start          ...           \\\n",
       "0           0.666667    AgamP3.chr2L    31   2403094          ...            \n",
       "1           0.857143    AgamP3.chr2L    65   2926448          ...            \n",
       "2           0.764706    AgamP3.chr2L    19   3249043          ...            \n",
       "3           0.714286    AgamP3.chr2L    43   5026458          ...            \n",
       "4           0.714286    AgamP3.chr2L    10   5861468          ...            \n",
       "5           0.619048    AgamP3.chr2L    25   6015462          ...            \n",
       "6           0.666667    AgamP3.chr2L    28   6045074          ...            \n",
       "7           0.700000    AgamP3.chr2L    34   6091202          ...            \n",
       "8           0.684211    AgamP3.chr2L    29   6491898          ...            \n",
       "9           0.476190    AgamP3.chr2L    32   6534100          ...            \n",
       "10          0.631579    AgamP3.chr2L    41   6717868          ...            \n",
       "11          0.476190    AgamP3.chr2L    20   6750932          ...            \n",
       "12          0.941176    AgamP3.chr2L    39   6796930          ...            \n",
       "13          0.894737    AgamP3.chr2L    50   6963036          ...            \n",
       "14          0.947368    AgamP3.chr2L    50   6969808          ...            \n",
       "15          0.619048    AgamP3.chr2L    40   6986385          ...            \n",
       "16          0.705882    AgamP3.chr2L    21   7248079          ...            \n",
       "17          0.736842    AgamP3.chr2L    34   7665920          ...            \n",
       "18          0.722222    AgamP3.chr2L    42   7676823          ...            \n",
       "19          0.944444    AgamP3.chr2L    46   7715076          ...            \n",
       "20          0.789474    AgamP3.chr2L    43   7856934          ...            \n",
       "21          0.789474    AgamP3.chr2L    54   7857227          ...            \n",
       "22          0.800000    AgamP3.chr2L    36   7885974          ...            \n",
       "23          0.736842    AgamP3.chr2L    35   8146115          ...            \n",
       "24          0.550000    AgamP3.chr2L    26   8226557          ...            \n",
       "25          0.789474    AgamP3.chr2L    49   8237055          ...            \n",
       "26          0.666667    AgamP3.chr2L    53   8774345          ...            \n",
       "27          0.800000    AgamP3.chr2L    24   9310873          ...            \n",
       "28          0.687500    AgamP3.chr2L    30   9350228          ...            \n",
       "29          0.842105    AgamP3.chr2L    38   9458076          ...            \n",
       "..               ...             ...   ...       ...          ...            \n",
       "633         0.733333     AgamP3.chrX    27   1144219          ...            \n",
       "634         0.666667     AgamP3.chrX    28   1815894          ...            \n",
       "635         0.866667     AgamP3.chrX    20   4194041          ...            \n",
       "636         0.928571     AgamP3.chrX    13   4692320          ...            \n",
       "637         0.700000     AgamP3.chrX    32  10000121          ...            \n",
       "638         0.866667     AgamP3.chrX    58  11953310          ...            \n",
       "639         0.928571     AgamP3.chrX    41  13338825          ...            \n",
       "640         0.785714     AgamP3.chrX    34  15479861          ...            \n",
       "641         0.833333     AgamP3.chrX    46  18453261          ...            \n",
       "642         0.750000     AgamP3.chrX    47  18742149          ...            \n",
       "643         0.578947     AgamP3.chrX    31  18759700          ...            \n",
       "644         0.764706  AgamP3.chrUNKN    41   1097580          ...            \n",
       "645         0.789474  AgamP3.chrUNKN    29   1181534          ...            \n",
       "646         0.823529  AgamP3.chrUNKN    40  10022361          ...            \n",
       "647         0.631579  AgamP3.chrUNKN    41  14190202          ...            \n",
       "648         0.684211  AgamP3.chrUNKN    49  14190202          ...            \n",
       "649         0.578947  AgamP3.chrUNKN    30  14190292          ...            \n",
       "650         0.684211  AgamP3.chrUNKN    38  14190292          ...            \n",
       "651         0.882353  AgamP3.chrUNKN    56  17272921          ...            \n",
       "652         0.846154  AgamP3.chrUNKN    26  17913483          ...            \n",
       "653         1.000000  AgamP3.chrUNKN    58  21709170          ...            \n",
       "654         0.666667  AgamP3.chrUNKN    27  22100036          ...            \n",
       "655         0.928571  AgamP3.chrUNKN    31  24502215          ...            \n",
       "656         0.850000  AgamP3.chrUNKN    41  30650492          ...            \n",
       "657         0.714286  AgamP3.chrUNKN    40  31107960          ...            \n",
       "658         0.809524  AgamP3.chrUNKN    43  31857478          ...            \n",
       "659         0.714286  AgamP3.chrUNKN    23  31857641          ...            \n",
       "660         0.894737  AgamP3.chrUNKN    18  31943410          ...            \n",
       "661         0.764706  AgamP3.chrUNKN    14  33274010          ...            \n",
       "662         0.769231  AgamP3.chrUNKN    30  38751128          ...            \n",
       "\n",
       "     target_snvs  target_start  \\\n",
       "0             21       2403145   \n",
       "1             52       2926537   \n",
       "2             13       3249077   \n",
       "3             35       5026511   \n",
       "4              8       5861515   \n",
       "5             11       6015528   \n",
       "6             19       6045125   \n",
       "7             17       6091291   \n",
       "8             23       6491957   \n",
       "9             21       6534177   \n",
       "10            34       6717911   \n",
       "11            11       6750980   \n",
       "12            33       6796958   \n",
       "13            44       6963081   \n",
       "14            44       6969853   \n",
       "15            21       6986481   \n",
       "16            13       7248156   \n",
       "17            25       7665983   \n",
       "18            32       7676860   \n",
       "19            36       7715116   \n",
       "20            35       7856966   \n",
       "21            45       7857272   \n",
       "22            27       7886034   \n",
       "23            28       8146154   \n",
       "24            18       8226616   \n",
       "25            40       8237124   \n",
       "26            40       8774409   \n",
       "27            20       9310913   \n",
       "28            22       9350274   \n",
       "29            29       9458114   \n",
       "..           ...           ...   \n",
       "633           20       1144261   \n",
       "634           15       1815984   \n",
       "635           12       4194088   \n",
       "636            4       4692359   \n",
       "637           21      10000169   \n",
       "638           49      11953359   \n",
       "639           32      13338883   \n",
       "640           26      15479905   \n",
       "641           37      18453308   \n",
       "642           30      18742234   \n",
       "643           19      18759759   \n",
       "644           33       1097618   \n",
       "645           22       1181591   \n",
       "646           31      10022415   \n",
       "647           26      14190278   \n",
       "648           36      14190278   \n",
       "649           14      14190351   \n",
       "650           24      14190351   \n",
       "651           43      17272987   \n",
       "652           20      17913523   \n",
       "653           54      21709207   \n",
       "654           13      22100120   \n",
       "655           24      24502303   \n",
       "656           33      30650530   \n",
       "657           27      31108001   \n",
       "658           24      31857533   \n",
       "659            5      31857754   \n",
       "660           16      31943447   \n",
       "661           11      33274053   \n",
       "662           24      38751177   \n",
       "\n",
       "                                          unid_species  \\\n",
       "0    [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "1    [{'AgamM1', 'AaraD1', 'AgamP3'}, {'AsteI2', 'A...   \n",
       "2    [{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "3    [{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...   \n",
       "4    [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "5    [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "6    [{'AdirW1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "7    [{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...   \n",
       "8    [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "9    [{'AfunF1', 'AdirW1', 'AmerM1', 'AgamP3', 'Ast...   \n",
       "10   [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "11   [{'AmelC1', 'AmerM1', 'AgamP3', 'AsteS1', 'Ast...   \n",
       "12                              [{'AgamM1', 'AgamP3'}]   \n",
       "13                    [{'AquaS1', 'AgamP3', 'AgamS1'}]   \n",
       "14                              [{'AquaS1', 'AgamS1'}]   \n",
       "15   [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "16   [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "17   [{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "18   [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "19                              [{'AaraD1', 'AgamP3'}]   \n",
       "20   [{'AgamM1', 'AquaS1', 'AgamP3', 'AgamS1'}, {'A...   \n",
       "21   [{'AgamM1', 'AquaS1', 'AaraD1', 'AgamP3'}, {'A...   \n",
       "22   [{'AgamM1', 'AquaS1', 'AmelC1', 'AgamS1'}, {'A...   \n",
       "23   [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "24   [{'AchrA1', 'AmerM1', 'AgamP3', 'AepiE1', 'Aar...   \n",
       "25   [{'AaraD1', 'AgamP3', 'AgamS1'}, {'AmelC1', 'A...   \n",
       "26   [{'AchrA1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "27          [{'AgamM1', 'AmerM1', 'AgamP3', 'AgamS1'}]   \n",
       "28   [{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...   \n",
       "29          [{'AgamM1', 'AquaS1', 'AaraD1', 'AgamS1'}]   \n",
       "..                                                 ...   \n",
       "633  [{'AgamM1', 'AgamP3', 'AgamS1'}, {'AquaS1', 'A...   \n",
       "634  [{'AmelC1', 'AgamP3', 'AaraD1', 'AquaS1', 'Aga...   \n",
       "635       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "636                             [{'AsteI2', 'AsteS1'}]   \n",
       "637  [{'AmelC1', 'AgamP3', 'AgamS1'}, {'AaraD1', 'A...   \n",
       "638       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "639                             [{'AsteI2', 'AsteS1'}]   \n",
       "640  [{'AgamM1', 'AgamP3', 'AgamS1'}, {'AsteI2', 'A...   \n",
       "641       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "642  [{'AgamM1', 'AgamP3', 'AgamS1'}, {'AquaS1', 'A...   \n",
       "643  [{'AmelC1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "644  [{'AquaS1', 'AmelC1', 'AgamP3', 'AgamS1'}, {'A...   \n",
       "645  [{'AgamM1', 'AaraD1', 'AgamP3', 'AgamS1'}, {'A...   \n",
       "646         [{'AgamM1', 'AmerM1', 'AgamP3', 'AgamS1'}]   \n",
       "647  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "648  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "649  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "650  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "651                   [{'AgamM1', 'AgamP3', 'AgamS1'}]   \n",
       "652       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "653                                                 []   \n",
       "654  [{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...   \n",
       "655                             [{'AsteI2', 'AsteS1'}]   \n",
       "656  [{'AquaS1', 'AgamP3', 'AgamS1'}, {'AsteI2', 'A...   \n",
       "657  [{'AmelC1', 'AmerM1', 'AgamP3', 'AgamM1', 'Aqu...   \n",
       "658  [{'AquaS1', 'AmelC1', 'AgamP3'}, {'AgamM1', 'A...   \n",
       "659  [{'AmerM1', 'AgamP3', 'AaraD1', 'AgamM1', 'Aqu...   \n",
       "660       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "661  [{'AgamM1', 'AmelC1', 'AaraD1', 'AgamS1'}, {'A...   \n",
       "662  [{'AgamM1', 'AaraD1', 'AgamS1'}, {'AsteI2', 'A...   \n",
       "\n",
       "                           exon                   gene intron  \\\n",
       "0    E013980A;E013980B;E013980C             AGAP004707   None   \n",
       "1             E014129A;E014130A             AGAP004734    Yes   \n",
       "2                          None                   None   None   \n",
       "3                      E014976A             AGAP004892   None   \n",
       "4                          None                   None   None   \n",
       "5                      E015082A             AGAP004919   None   \n",
       "6                          None                   None   None   \n",
       "7                      E015094A             AGAP004923   None   \n",
       "8                          None                   None   None   \n",
       "9             E015172A;E015175B             AGAP004943   None   \n",
       "10                         None                   None   None   \n",
       "11                         None                   None   None   \n",
       "12                         None                   None   None   \n",
       "13                         None             AGAP004950   None   \n",
       "14                         None             AGAP004950   None   \n",
       "15                     E015199A             AGAP004950   None   \n",
       "16                         None                   None   None   \n",
       "17                         None                   None   None   \n",
       "18                         None                   None   None   \n",
       "19                         None                   None   None   \n",
       "20                         None             AGAP005008   None   \n",
       "21                         None             AGAP005008   None   \n",
       "22                         None             AGAP005008   None   \n",
       "23                         None                   None   None   \n",
       "24                         None                   None   None   \n",
       "25                         None                   None   None   \n",
       "26            E015672A;E015672B             AGAP005043   None   \n",
       "27                         None                   None   None   \n",
       "28                         None                   None   None   \n",
       "29                         None                   None   None   \n",
       "..                          ...                    ...    ...   \n",
       "633                        None                   None   None   \n",
       "634           E000519B;E000519A  AGAP000112;AGAP000113   None   \n",
       "635                        None             AGAP000225   None   \n",
       "636                        None                   None   None   \n",
       "637  E002410A;E002410C;E054460B             AGAP000562   None   \n",
       "638                        None                   None   None   \n",
       "639                        None                   None   None   \n",
       "640                        None                   None   None   \n",
       "641                        None             AGAP000962   None   \n",
       "642                    E003998A             AGAP000974   None   \n",
       "643                    E004008A             AGAP000974   None   \n",
       "644                        None                   None   None   \n",
       "645                        None                   None   None   \n",
       "646                        None                   None   None   \n",
       "647                    E012883A             AGAP012545   None   \n",
       "648                    E012883A             AGAP012545   None   \n",
       "649                    E012883A             AGAP012545   None   \n",
       "650                    E012883A             AGAP012545   None   \n",
       "651                        None                   None   None   \n",
       "652                        None                   None   None   \n",
       "653                        None                   None   None   \n",
       "654                        None                   None   None   \n",
       "655                        None                   None   None   \n",
       "656                        None                   None   None   \n",
       "657                        None                   None   None   \n",
       "658                        None                   None   None   \n",
       "659                        None                   None   None   \n",
       "660                        None                   None   None   \n",
       "661                        None                   None   None   \n",
       "662                        None                   None   None   \n",
       "\n",
       "                                          mRNA repeat   utr  \\\n",
       "0    AGAP004707-RA;AGAP004707-RB;AGAP004707-RC   None  None   \n",
       "1                                AGAP004734-RA   None  None   \n",
       "2                                         None   None  None   \n",
       "3                                AGAP004892-RA   None  None   \n",
       "4                                         None   None  None   \n",
       "5                                AGAP004919-RA   None   Yes   \n",
       "6                                         None   None  None   \n",
       "7                                AGAP004923-RA   None  None   \n",
       "8                                         None   None  None   \n",
       "9                  AGAP004943-RA;AGAP004943-RB   None  None   \n",
       "10                                        None   None  None   \n",
       "11                                        None   None  None   \n",
       "12                                        None   None  None   \n",
       "13                               AGAP004950-RA   None  None   \n",
       "14                               AGAP004950-RA   None  None   \n",
       "15                               AGAP004950-RA   None  None   \n",
       "16                                        None   None  None   \n",
       "17                                        None   None  None   \n",
       "18                                        None   None  None   \n",
       "19                                        None   None  None   \n",
       "20                 AGAP005008-RA;AGAP005008-RB   None  None   \n",
       "21                 AGAP005008-RA;AGAP005008-RB   None  None   \n",
       "22                 AGAP005008-RA;AGAP005008-RB   None  None   \n",
       "23                                        None   None  None   \n",
       "24                                        None   None  None   \n",
       "25                                        None   None  None   \n",
       "26                 AGAP005043-RA;AGAP005043-RB   None  None   \n",
       "27                                        None   None  None   \n",
       "28                                        None   None  None   \n",
       "29                                        None   None  None   \n",
       "..                                         ...    ...   ...   \n",
       "633                                       None   None  None   \n",
       "634  AGAP000112-RA;AGAP000113-RB;AGAP000113-RA   None  None   \n",
       "635                              AGAP000225-RA   None  None   \n",
       "636                                       None   None  None   \n",
       "637  AGAP000562-RA;AGAP000562-RC;AGAP000562-RB   None  None   \n",
       "638                                       None   None  None   \n",
       "639                                       None   None  None   \n",
       "640                                       None   None  None   \n",
       "641                              AGAP000962-RA   None  None   \n",
       "642                              AGAP000974-RA   None  None   \n",
       "643                              AGAP000974-RA   None  None   \n",
       "644                                       None   None  None   \n",
       "645                                       None   None  None   \n",
       "646                                       None   None  None   \n",
       "647                              AGAP012545-RA   None  None   \n",
       "648                              AGAP012545-RA   None  None   \n",
       "649                              AGAP012545-RA   None  None   \n",
       "650                              AGAP012545-RA   None  None   \n",
       "651                                       None   None  None   \n",
       "652                                       None   None  None   \n",
       "653                                       None   None  None   \n",
       "654                                       None   None  None   \n",
       "655                                       None   None  None   \n",
       "656                                       None   None  None   \n",
       "657                                       None   None  None   \n",
       "658                                       None   None  None   \n",
       "659                                       None   None  None   \n",
       "660                                       None   None  None   \n",
       "661                                       None   None  None   \n",
       "662                                       None   None  None   \n",
       "\n",
       "    id lineage proportion  \n",
       "0                0.666667  \n",
       "1                0.857143  \n",
       "2                0.764706  \n",
       "3                0.714286  \n",
       "4                0.714286  \n",
       "5                0.619048  \n",
       "6                0.666667  \n",
       "7                0.700000  \n",
       "8                0.684211  \n",
       "9                0.476190  \n",
       "10               0.631579  \n",
       "11               0.476190  \n",
       "12               0.941176  \n",
       "13               0.894737  \n",
       "14               0.947368  \n",
       "15               0.619048  \n",
       "16               0.705882  \n",
       "17               0.736842  \n",
       "18               0.722222  \n",
       "19               0.944444  \n",
       "20               0.789474  \n",
       "21               0.789474  \n",
       "22               0.800000  \n",
       "23               0.736842  \n",
       "24               0.550000  \n",
       "25               0.789474  \n",
       "26               0.666667  \n",
       "27               0.800000  \n",
       "28               0.687500  \n",
       "29               0.842105  \n",
       "..                    ...  \n",
       "633              0.733333  \n",
       "634              0.666667  \n",
       "635              0.866667  \n",
       "636              0.928571  \n",
       "637              0.700000  \n",
       "638              0.866667  \n",
       "639              0.928571  \n",
       "640              0.785714  \n",
       "641              0.833333  \n",
       "642              0.750000  \n",
       "643              0.578947  \n",
       "644              0.764706  \n",
       "645              0.789474  \n",
       "646              0.823529  \n",
       "647              0.631579  \n",
       "648              0.684211  \n",
       "649              0.578947  \n",
       "650              0.684211  \n",
       "651              0.882353  \n",
       "652              0.846154  \n",
       "653              1.000000  \n",
       "654              0.666667  \n",
       "655              0.928571  \n",
       "656              0.850000  \n",
       "657              0.714286  \n",
       "658              0.809524  \n",
       "659              0.714286  \n",
       "660              0.894737  \n",
       "661              0.764706  \n",
       "662              0.769231  \n",
       "\n",
       "[663 rows x 23 columns]"
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load metadata\n",
    "init_meta = pd.read_csv(META_FILE, index_col=0)\n",
    "init_meta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(663, 47)"
      ]
     },
     "execution_count": 62,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# combine metadata\n",
    "comb_meta = pd.concat([init_meta, pd.DataFrame(bd).T], axis=1)\n",
    "comb_meta.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['aligned_len', 'aligned_species', 'chr', 'end', 'id_lineages', 'indels',\n",
       "       'informativeness', 'seqid', 'snvs', 'start', 'target_aligned_len',\n",
       "       'target_end', 'target_indels', 'target_snvs', 'target_start',\n",
       "       'unid_species', 'exon', 'gene', 'intron', 'mRNA', 'repeat', 'utr',\n",
       "       'id lineage proportion', 'AaegL5_expect', 'AaegL5_hits',\n",
       "       'AaegL5_identity', 'AaegL5_length', 'AaegL5_q_span', 'AaegL5_s_span',\n",
       "       'AgamP3_expect', 'AgamP3_hits', 'AgamP3_identity', 'AgamP3_length',\n",
       "       'AgamP3_q_span', 'AgamP3_s_span', 'BDGP6_expect', 'BDGP6_hits',\n",
       "       'BDGP6_identity', 'BDGP6_length', 'BDGP6_q_span', 'BDGP6_s_span',\n",
       "       'CpipJ2_expect', 'CpipJ2_hits', 'CpipJ2_identity', 'CpipJ2_length',\n",
       "       'CpipJ2_q_span', 'CpipJ2_s_span'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 63,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "comb_meta.columns"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Add forgotten data from alignment - unaln_species"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['AgamP3',\n",
       " 'AgamS1',\n",
       " 'AgamM1',\n",
       " 'AmerM1',\n",
       " 'AaraD1',\n",
       " 'AquaS1',\n",
       " 'AmelC1',\n",
       " 'AchrA1',\n",
       " 'AepiE1',\n",
       " 'AminM1',\n",
       " 'AculA1',\n",
       " 'AfunF1',\n",
       " 'AsteS1',\n",
       " 'AsteI2',\n",
       " 'AmacM1',\n",
       " 'AfarF1',\n",
       " 'AdirW1',\n",
       " 'AsinS1',\n",
       " 'AatrE1',\n",
       " 'AdarC2',\n",
       " 'AalbS1']"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# list of all species\n",
    "all_sp = []\n",
    "for aln in AlignIO.parse(AMPL_FILE, \"maf\"):\n",
    "    if len(aln) == 21:\n",
    "        all_sp = [seq.id.split('.')[0] for seq in aln]\n",
    "    break\n",
    "all_sp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'AfunF1;AmacM1;AfarF1;AdirW1;AsinS1;AatrE1;AdarC2;AalbS1'"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# unaligned species per amplicon\n",
    "unaln = dict()\n",
    "i = 0\n",
    "for aln in AlignIO.parse(AMPL_FILE, \"maf\"):\n",
    "    aln_sp = [seq.id.split('.')[0] for seq in aln]\n",
    "    unaln[i] = ';'.join([sp for sp in all_sp if sp not in aln_sp])\n",
    "    i+=1\n",
    "unaln[662]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>aligned_len</th>\n",
       "      <th>aligned_species</th>\n",
       "      <th>chr</th>\n",
       "      <th>end</th>\n",
       "      <th>id_lineages</th>\n",
       "      <th>indels</th>\n",
       "      <th>informativeness</th>\n",
       "      <th>seqid</th>\n",
       "      <th>snvs</th>\n",
       "      <th>start</th>\n",
       "      <th>...</th>\n",
       "      <th>BDGP6_length</th>\n",
       "      <th>BDGP6_q_span</th>\n",
       "      <th>BDGP6_s_span</th>\n",
       "      <th>CpipJ2_expect</th>\n",
       "      <th>CpipJ2_hits</th>\n",
       "      <th>CpipJ2_identity</th>\n",
       "      <th>CpipJ2_length</th>\n",
       "      <th>CpipJ2_q_span</th>\n",
       "      <th>CpipJ2_s_span</th>\n",
       "      <th>unaligned_species</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>185</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>2403278</td>\n",
       "      <td>14</td>\n",
       "      <td>5</td>\n",
       "      <td>0.666667</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>31</td>\n",
       "      <td>2403094</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.87203e-73</td>\n",
       "      <td>1</td>\n",
       "      <td>0.9402173913043478</td>\n",
       "      <td>184</td>\n",
       "      <td>1-184</td>\n",
       "      <td>supercont3.1170:126707-126524</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>345</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>2926735</td>\n",
       "      <td>18</td>\n",
       "      <td>96</td>\n",
       "      <td>0.857143</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>65</td>\n",
       "      <td>2926448</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.43691e-64</td>\n",
       "      <td>1</td>\n",
       "      <td>0.8333333333333334</td>\n",
       "      <td>288</td>\n",
       "      <td>1-286</td>\n",
       "      <td>supercont3.35:120152-120424</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>199</td>\n",
       "      <td>17</td>\n",
       "      <td>2L</td>\n",
       "      <td>3249178</td>\n",
       "      <td>13</td>\n",
       "      <td>108</td>\n",
       "      <td>0.764706</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>19</td>\n",
       "      <td>3249043</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AsinS1;AatrE1;AdarC2;AalbS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>234</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>5026687</td>\n",
       "      <td>15</td>\n",
       "      <td>5</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>43</td>\n",
       "      <td>5026458</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>321</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>5861628</td>\n",
       "      <td>15</td>\n",
       "      <td>191</td>\n",
       "      <td>0.714286</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>10</td>\n",
       "      <td>5861468</td>\n",
       "      <td>...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 48 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   aligned_len  aligned_species chr      end  id_lineages  indels  \\\n",
       "0          185               21  2L  2403278           14       5   \n",
       "1          345               21  2L  2926735           18      96   \n",
       "2          199               17  2L  3249178           13     108   \n",
       "3          234               21  2L  5026687           15       5   \n",
       "4          321               21  2L  5861628           15     191   \n",
       "\n",
       "   informativeness         seqid  snvs    start             ...               \\\n",
       "0         0.666667  AgamP3.chr2L    31  2403094             ...                \n",
       "1         0.857143  AgamP3.chr2L    65  2926448             ...                \n",
       "2         0.764706  AgamP3.chr2L    19  3249043             ...                \n",
       "3         0.714286  AgamP3.chr2L    43  5026458             ...                \n",
       "4         0.714286  AgamP3.chr2L    10  5861468             ...                \n",
       "\n",
       "   BDGP6_length  BDGP6_q_span  BDGP6_s_span  CpipJ2_expect  CpipJ2_hits  \\\n",
       "0           NaN           NaN           NaN    1.87203e-73            1   \n",
       "1           NaN           NaN           NaN    2.43691e-64            1   \n",
       "2           NaN           NaN           NaN            NaN          NaN   \n",
       "3           NaN           NaN           NaN            NaN          NaN   \n",
       "4           NaN           NaN           NaN            NaN          NaN   \n",
       "\n",
       "      CpipJ2_identity CpipJ2_length CpipJ2_q_span  \\\n",
       "0  0.9402173913043478           184         1-184   \n",
       "1  0.8333333333333334           288         1-286   \n",
       "2                 NaN           NaN           NaN   \n",
       "3                 NaN           NaN           NaN   \n",
       "4                 NaN           NaN           NaN   \n",
       "\n",
       "                   CpipJ2_s_span            unaligned_species  \n",
       "0  supercont3.1170:126707-126524                               \n",
       "1    supercont3.35:120152-120424                               \n",
       "2                            NaN  AsinS1;AatrE1;AdarC2;AalbS1  \n",
       "3                            NaN                               \n",
       "4                            NaN                               \n",
       "\n",
       "[5 rows x 48 columns]"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# add to metadata\n",
    "comb_meta['unaligned_species'] = pd.Series(unaln)\n",
    "comb_meta.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Remove markers duplicated in agam"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(591, 48)"
      ]
     },
     "execution_count": 74,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 72 markers were removed as duplicates in agam\n",
    "comb_meta = comb_meta[comb_meta['AgamP3_hits'] == 1]\n",
    "comb_meta.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "591\r\n"
     ]
    }
   ],
   "source": [
    "# write filtered alignment \n",
    "i = 0\n",
    "with open(UPD_AMPL_FILE, \"w\") as o:\n",
    "    for aln in AlignIO.parse(AMPL_FILE, \"maf\"):\n",
    "        if i in comb_meta.index:\n",
    "            AlignIO.write(aln, o, \"maf\")\n",
    "        i += 1\n",
    "! grep -c 'AgamP3' {UPD_AMPL_FILE}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "RangeIndex(start=0, stop=591, step=1)"
      ]
     },
     "execution_count": 76,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# reset index for compatibility with filtered alignment\n",
    "comb_meta.reset_index(drop=True, inplace=True)\n",
    "comb_meta.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Reorder columns and save"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(591, 47)"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# reorder and rename columns\n",
    "comb_meta = comb_meta[['chr', 'start', 'end', 'seqid', # agam coordinates\n",
    "            'aligned_species', 'unaligned_species', 'aligned_len', 'indels', 'snvs', # amplicon stats\n",
    "            'target_start', 'target_end', 'target_aligned_len', 'target_indels', 'target_snvs', # target stats\n",
    "            'id_lineages', 'informativeness', 'unid_species', # identification power\n",
    "            'exon', 'gene', 'intron', 'mRNA', 'repeat', 'utr', # agam annotations\n",
    "            'AgamP3_hits', 'AgamP3_length', 'AgamP3_identity', \n",
    "            'AgamP3_q_span', 'AgamP3_s_span', 'AgamP3_expect', # agam blast\n",
    "            'AaegL5_hits', 'AaegL5_length', 'AaegL5_identity',\n",
    "            'AaegL5_q_span', 'AaegL5_s_span', 'AaegL5_expect', # aedes blast\n",
    "            'CpipJ2_hits', 'CpipJ2_length', 'CpipJ2_identity', \n",
    "            'CpipJ2_q_span', 'CpipJ2_s_span', 'CpipJ2_expect', # culex blast\n",
    "            'BDGP6_hits', 'BDGP6_length', 'BDGP6_identity', \n",
    "            'BDGP6_q_span', 'BDGP6_s_span','BDGP6_expect' # drosophila blast\n",
    "            #'id lineage proportion' # duplicate to informativeness, remove\n",
    "            ]]\n",
    "comb_meta = comb_meta.rename(columns={\"aligned_species\": \"num_aligned_species\", \n",
    "                              \"indels\": \"total_indels\",\n",
    "                              \"snvs\": \"total_snvs\",\n",
    "                              \"id_lineages\":\"num_id_lineages\",\n",
    "                              \"informativeness\": \"prop_id_lineages\"\n",
    "                             })\n",
    "comb_meta.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [],
   "source": [
    "comb_meta.to_excel(UPD_META_FILE)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Sandbox"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/am60/miniconda3/envs/biipy/lib/python3.5/site-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.\n",
      "  BiopythonExperimentalWarning)\n",
      "/Users/am60/miniconda3/envs/biipy/lib/python3.5/site-packages/Bio/SearchIO/BlastIO/blast_xml.py:336: BiopythonParserWarning: Renaming hit ID '2R' to a BLAST-generated ID 'gnl|BL_ORD_ID|2318' since the ID was already matched by your query '129'. Your BLAST database may contain duplicate entries.\n",
      "  (hit.id, hit.blast_id, query_id), BiopythonParserWarning)\n",
      "/Users/am60/miniconda3/envs/biipy/lib/python3.5/site-packages/Bio/SearchIO/BlastIO/blast_xml.py:336: BiopythonParserWarning: Renaming hit ID '2R' to a BLAST-generated ID 'gnl|BL_ORD_ID|2318' since the ID was already matched by your query '278'. Your BLAST database may contain duplicate entries.\n",
      "  (hit.id, hit.blast_id, query_id), BiopythonParserWarning)\n",
      "/Users/am60/miniconda3/envs/biipy/lib/python3.5/site-packages/Bio/SearchIO/BlastIO/blast_xml.py:336: BiopythonParserWarning: Renaming hit ID '2R' to a BLAST-generated ID 'gnl|BL_ORD_ID|2318' since the ID was already matched by your query '279'. Your BLAST database may contain duplicate entries.\n",
      "  (hit.id, hit.blast_id, query_id), BiopythonParserWarning)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Query: 129 \n",
      "        Hit: 2L chromosome:AgamP3:2L:1:49364325:1\n",
      "Query range: [0:343] (1)\n",
      "  Hit range: [46338833:46339176] (1)\n",
      "Quick stats: evalue 7e-180; bitscore 634.52\n",
      "  Fragments: 1 (343 columns)\n",
      "     Query - CATCAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACT~~~GTGCC\n",
      "             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~|||||\n",
      "       Hit - CATCAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACT~~~GTGCC\n",
      "      Query: 129 \n",
      "        Hit: supercont3.222 dna:supercontig supercontig:CpipJ2:supercont3.222...\n",
      "Query range: [2:343] (1)\n",
      "  Hit range: [571656:571997] (-1)\n",
      "Quick stats: evalue 2.1e-140; bitscore 503.41\n",
      "  Fragments: 1 (341 columns)\n",
      "     Query - TCAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCT~~~GTGCC\n",
      "             |||| ||||||||||| ||||||||||||||||| ||||| || ||||||||||| || ~~~|||||\n",
      "       Hit - TCAAGATGGGTAAGGAAAAGACTCATATTAACATTGTCGTGATTGGACACGTCGATTCC~~~GTGCC\n",
      "      Query: 129 \n",
      "        Hit: 2R chromosome:AgamP3:2R:1:61545105:1\n",
      "Query range: [3:343] (1)\n",
      "  Hit range: [39348406:39348746] (1)\n",
      "Quick stats: evalue 3.4e-138; bitscore 496.02\n",
      "  Fragments: 1 (340 columns)\n",
      "     Query - CAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCTG~~~GTGCC\n",
      "             || |||||| ||||||||||||||||||||||||||||||||||| ||||||||||| |~~~|||||\n",
      "       Hit - CAGAATGGGAAAGGAGAAGACTCATATTAACATCGTCGTCATCGGTCACGTCGACTCCG~~~GTGCC\n",
      "      Query: 129 \n",
      "        Hit: supercont3.245 dna:supercontig supercontig:CpipJ2:supercont3.245...\n",
      "Query range: [7:343] (1)\n",
      "  Hit range: [267777:268113] (1)\n",
      "Quick stats: evalue 5.8e-131; bitscore 472.02\n",
      "  Fragments: 1 (336 columns)\n",
      "     Query - ATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCTGGCAA~~~GTGCC\n",
      "             |||||||||||||||| |||||| |||||||||||||||||||||||||| || |||||~~~|||||\n",
      "       Hit - ATGGGTAAGGAGAAGATTCATATCAACATCGTCGTCATCGGACACGTCGATTCCGGCAA~~~GTGCC\n",
      "      Query: 129 \n",
      "        Hit: 3 dna:chromosome chromosome:AaegL5:3:1:409777670:1\n",
      "Query range: [7:343] (1)\n",
      "  Hit range: [25283676:25284012] (-1)\n",
      "Quick stats: evalue 5.8e-131; bitscore 472.02\n",
      "  Fragments: 1 (336 columns)\n",
      "     Query - ATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCTGGCAA~~~GTGCC\n",
      "             |||||||||||||||| ||||||||||||||||||||| ||||||||||| || |||||~~~|||||\n",
      "       Hit - ATGGGTAAGGAGAAGATTCATATTAACATCGTCGTCATTGGACACGTCGATTCCGGCAA~~~GTGCC\n",
      "      Query: 129 \n",
      "        Hit: 2 dna:chromosome chromosome:AaegL5:2:1:474425716:1\n",
      "Query range: [3:343] (1)\n",
      "  Hit range: [45578027:45578367] (-1)\n",
      "Quick stats: evalue 1.6e-126; bitscore 457.24\n",
      "  Fragments: 1 (340 columns)\n",
      "     Query - CAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCTG~~~GTGCC\n",
      "             ||| ||||||||||||||||||||||||||||| ||||| || ||||||||||| ||||~~~| |||\n",
      "       Hit - CAAGATGGGTAAGGAGAAGACTCATATTAACATTGTCGTAATTGGACACGTCGATTCTG~~~GCGCC\n",
      "      Query: 129 \n",
      "        Hit: gnl|BL_ORD_ID|2318 2R dna_sm:chromosome chromosome:BDGP6:2R:1:25...\n",
      "Query range: [0:343] (1)\n",
      "  Hit range: [11893566:11893910] (1)\n",
      "Quick stats: evalue 1.7e-111; bitscore 407.38\n",
      "  Fragments: 1 (344 columns)\n",
      "     Query - CAT-CAAAATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGAC~~~GTGCC\n",
      "             ||| ||| ||||| ||||| |||| ||| |||||||| ||||| |||||||||||||| ~~~| |||\n",
      "       Hit - CATCCAACATGGGCAAGGAAAAGATTCACATTAACATTGTCGTGATCGGACACGTCGAT~~~GCGCC\n",
      "      Query: 129 \n",
      "        Hit: 3R dna_sm:chromosome chromosome:BDGP6:3R:1:32079331:1 REF\n",
      "Query range: [7:342] (1)\n",
      "  Hit range: [31740346:31740681] (1)\n",
      "Quick stats: evalue 1e-103; bitscore 381.53\n",
      "  Fragments: 1 (335 columns)\n",
      "     Query - ATGGGTAAGGAGAAGACTCATATTAACATCGTCGTCATCGGACACGTCGACTCTGGCAA~~~TGTGC\n",
      "             ||||| ||||||||||  ||||||||||| || ||||| || || || ||||| |||||~~~|||||\n",
      "       Hit - ATGGGCAAGGAGAAGATCCATATTAACATTGTGGTCATTGGCCATGTGGACTCCGGCAA~~~TGTGC\n"
     ]
    }
   ],
   "source": [
    "# parse hits with SearchIO - it does not extract identities/matches\n",
    "from Bio import SearchIO\n",
    "blast_qresult = list(SearchIO.parse(BLAST_FILE, \"blast-xml\"))\n",
    "for hit in blast_qresult[129]: \n",
    "    for hsp in hit:\n",
    "        print(hsp)\n",
    "#hierarchy results->hit->hsp->hsp_framgent"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is an example of 'bad' marker - multiple hits in three of four genomes. Other informative measures - % query coverage and % identity for each hit.\n",
    "\n",
    "Warnings generated during parsing result from same chromosome names in different genomes: here it was 2R in Agam and Dmel. Need to take into account the additional field."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>aligned_len</th>\n",
       "      <th>aligned_species</th>\n",
       "      <th>chr</th>\n",
       "      <th>end</th>\n",
       "      <th>id_lineages</th>\n",
       "      <th>indels</th>\n",
       "      <th>informativeness</th>\n",
       "      <th>seqid</th>\n",
       "      <th>snvs</th>\n",
       "      <th>...</th>\n",
       "      <th>target_snvs</th>\n",
       "      <th>target_start</th>\n",
       "      <th>unid_species</th>\n",
       "      <th>exon</th>\n",
       "      <th>gene</th>\n",
       "      <th>intron</th>\n",
       "      <th>mRNA</th>\n",
       "      <th>repeat</th>\n",
       "      <th>utr</th>\n",
       "      <th>id lineage proportion</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>345</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>2926735</td>\n",
       "      <td>18</td>\n",
       "      <td>96</td>\n",
       "      <td>0.857143</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>65</td>\n",
       "      <td>...</td>\n",
       "      <td>52</td>\n",
       "      <td>2926537</td>\n",
       "      <td>[{'AgamM1', 'AaraD1', 'AgamP3'}, {'AsteI2', 'A...</td>\n",
       "      <td>E014129A;E014130A</td>\n",
       "      <td>AGAP004734</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP004734-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.857143</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>33</td>\n",
       "      <td>298</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>10356642</td>\n",
       "      <td>20</td>\n",
       "      <td>139</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>38</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>10356481</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E016098A;E016099A</td>\n",
       "      <td>AGAP005134</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP005134-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>79</th>\n",
       "      <td>79</td>\n",
       "      <td>338</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>26760891</td>\n",
       "      <td>20</td>\n",
       "      <td>157</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>47</td>\n",
       "      <td>...</td>\n",
       "      <td>40</td>\n",
       "      <td>26760778</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}]</td>\n",
       "      <td>E020405C;E020406C;E020405B;E020406B;E020405A;E...</td>\n",
       "      <td>AGAP006107</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP006107-RC;AGAP006107-RB;AGAP006107-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>85</th>\n",
       "      <td>85</td>\n",
       "      <td>322</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>27674840</td>\n",
       "      <td>20</td>\n",
       "      <td>178</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>35</td>\n",
       "      <td>...</td>\n",
       "      <td>20</td>\n",
       "      <td>27674693</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E020688A;E020689A;E020688B;E020689B</td>\n",
       "      <td>AGAP006176</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP006176-RA;AGAP006176-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101</th>\n",
       "      <td>101</td>\n",
       "      <td>376</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>34301269</td>\n",
       "      <td>20</td>\n",
       "      <td>159</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>51</td>\n",
       "      <td>...</td>\n",
       "      <td>32</td>\n",
       "      <td>34301104</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E022297D;E022298D;E022297C;E022298C;E022297B;E...</td>\n",
       "      <td>AGAP006590</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP006590-RD;AGAP006590-RC;AGAP006590-RB;AGAP...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>118</th>\n",
       "      <td>118</td>\n",
       "      <td>488</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>42393512</td>\n",
       "      <td>20</td>\n",
       "      <td>137</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>65</td>\n",
       "      <td>...</td>\n",
       "      <td>47</td>\n",
       "      <td>42393238</td>\n",
       "      <td>[]</td>\n",
       "      <td>E024360A;E024361A</td>\n",
       "      <td>AGAP007086</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007086-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119</th>\n",
       "      <td>119</td>\n",
       "      <td>591</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>42393789</td>\n",
       "      <td>20</td>\n",
       "      <td>183</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>55</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>42393509</td>\n",
       "      <td>[]</td>\n",
       "      <td>E024361A;E024362A</td>\n",
       "      <td>AGAP007086</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007086-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120</th>\n",
       "      <td>120</td>\n",
       "      <td>291</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>42542495</td>\n",
       "      <td>11</td>\n",
       "      <td>17</td>\n",
       "      <td>0.550000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>30</td>\n",
       "      <td>...</td>\n",
       "      <td>12</td>\n",
       "      <td>42542260</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aqu...</td>\n",
       "      <td>E024408A;E024409A</td>\n",
       "      <td>AGAP007092</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007092-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.550000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>128</td>\n",
       "      <td>419</td>\n",
       "      <td>20</td>\n",
       "      <td>2L</td>\n",
       "      <td>45853080</td>\n",
       "      <td>19</td>\n",
       "      <td>159</td>\n",
       "      <td>0.950000</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>22</td>\n",
       "      <td>...</td>\n",
       "      <td>6</td>\n",
       "      <td>45852918</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E025379B;E025380B;E025379A;E025380A</td>\n",
       "      <td>AGAP007340</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007340-RB;AGAP007340-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.950000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>133</th>\n",
       "      <td>133</td>\n",
       "      <td>283</td>\n",
       "      <td>21</td>\n",
       "      <td>2L</td>\n",
       "      <td>48612732</td>\n",
       "      <td>20</td>\n",
       "      <td>149</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2L</td>\n",
       "      <td>27</td>\n",
       "      <td>...</td>\n",
       "      <td>16</td>\n",
       "      <td>48612544</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E026619C;E026620C;E026619D;E026620D;E026619A;E...</td>\n",
       "      <td>AGAP007643</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007643-RC;AGAP007643-RD;AGAP007643-RA;AGAP...</td>\n",
       "      <td>None</td>\n",
       "      <td>Yes</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>151</th>\n",
       "      <td>151</td>\n",
       "      <td>186</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>3879160</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>0.600000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>28</td>\n",
       "      <td>...</td>\n",
       "      <td>16</td>\n",
       "      <td>3879042</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Afa...</td>\n",
       "      <td>E039025A;E056936B;E053755B</td>\n",
       "      <td>AGAP001370</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001370-RA;AGAP001370-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.600000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>152</th>\n",
       "      <td>152</td>\n",
       "      <td>324</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>3879298</td>\n",
       "      <td>13</td>\n",
       "      <td>0</td>\n",
       "      <td>0.650000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>50</td>\n",
       "      <td>...</td>\n",
       "      <td>34</td>\n",
       "      <td>3879042</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>E039025A;E056936B;E053755B</td>\n",
       "      <td>AGAP001370</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001370-RA;AGAP001370-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.650000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>153</th>\n",
       "      <td>153</td>\n",
       "      <td>251</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>3879298</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>0.600000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>40</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>3879096</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...</td>\n",
       "      <td>E039025A;E056936B;E053755B</td>\n",
       "      <td>AGAP001370</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001370-RA;AGAP001370-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.600000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>183</th>\n",
       "      <td>183</td>\n",
       "      <td>311</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>7053447</td>\n",
       "      <td>21</td>\n",
       "      <td>135</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>36</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>7053270</td>\n",
       "      <td>[]</td>\n",
       "      <td>E040220A;E040221A</td>\n",
       "      <td>AGAP001632</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001632-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>186</th>\n",
       "      <td>186</td>\n",
       "      <td>473</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>8504834</td>\n",
       "      <td>18</td>\n",
       "      <td>96</td>\n",
       "      <td>0.900000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>77</td>\n",
       "      <td>...</td>\n",
       "      <td>49</td>\n",
       "      <td>8504608</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E053266B;E040564B;E053266A;E040564A</td>\n",
       "      <td>AGAP001690</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001690-RB;AGAP001690-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>189</th>\n",
       "      <td>189</td>\n",
       "      <td>408</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>10593923</td>\n",
       "      <td>16</td>\n",
       "      <td>169</td>\n",
       "      <td>0.761905</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>43</td>\n",
       "      <td>...</td>\n",
       "      <td>20</td>\n",
       "      <td>10593690</td>\n",
       "      <td>[{'AgamM1', 'AaraD1', 'AgamP3'}, {'AmelC1', 'A...</td>\n",
       "      <td>E041043B;E041044B;E041043A;E041044A</td>\n",
       "      <td>AGAP001799</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP001799-RB;AGAP001799-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.761905</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>204</td>\n",
       "      <td>414</td>\n",
       "      <td>19</td>\n",
       "      <td>2R</td>\n",
       "      <td>16469958</td>\n",
       "      <td>18</td>\n",
       "      <td>181</td>\n",
       "      <td>0.947368</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>41</td>\n",
       "      <td>...</td>\n",
       "      <td>38</td>\n",
       "      <td>16469779</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E042394A;E042395A;E042394B;E042395B</td>\n",
       "      <td>AGAP002150</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP002150-RA;AGAP002150-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.947368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>211</th>\n",
       "      <td>211</td>\n",
       "      <td>324</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>16889800</td>\n",
       "      <td>17</td>\n",
       "      <td>3</td>\n",
       "      <td>0.809524</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>56</td>\n",
       "      <td>...</td>\n",
       "      <td>39</td>\n",
       "      <td>16889615</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AgamP3', 'AgamS1'}, {'A...</td>\n",
       "      <td>E042536A;E053752A</td>\n",
       "      <td>AGAP002172</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP002172-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.809524</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>216</th>\n",
       "      <td>216</td>\n",
       "      <td>401</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>20528316</td>\n",
       "      <td>20</td>\n",
       "      <td>167</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>53</td>\n",
       "      <td>...</td>\n",
       "      <td>42</td>\n",
       "      <td>20528121</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E043230B;E043231B;E043230A;E043231A;E043230E;E...</td>\n",
       "      <td>AGAP002350</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP002350-RB;AGAP002350-RA;AGAP002350-RE;AGAP...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>231</th>\n",
       "      <td>231</td>\n",
       "      <td>353</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>26654806</td>\n",
       "      <td>20</td>\n",
       "      <td>145</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>49</td>\n",
       "      <td>...</td>\n",
       "      <td>36</td>\n",
       "      <td>26654601</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E044960A;E044962A</td>\n",
       "      <td>AGAP002748</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP002748-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>237</th>\n",
       "      <td>237</td>\n",
       "      <td>272</td>\n",
       "      <td>21</td>\n",
       "      <td>2R</td>\n",
       "      <td>27902640</td>\n",
       "      <td>20</td>\n",
       "      <td>125</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>28</td>\n",
       "      <td>...</td>\n",
       "      <td>21</td>\n",
       "      <td>27902493</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E045221A;E045222A;E057892B;E045222B</td>\n",
       "      <td>AGAP002814</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP002814-RA;AGAP002814-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>269</th>\n",
       "      <td>269</td>\n",
       "      <td>281</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>36019728</td>\n",
       "      <td>18</td>\n",
       "      <td>119</td>\n",
       "      <td>0.900000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>49</td>\n",
       "      <td>...</td>\n",
       "      <td>37</td>\n",
       "      <td>36019603</td>\n",
       "      <td>[{'AgamP3', 'AgamS1'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E047321A;E054664A</td>\n",
       "      <td>AGAP003327</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP003327-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>306</td>\n",
       "      <td>309</td>\n",
       "      <td>20</td>\n",
       "      <td>2R</td>\n",
       "      <td>47760981</td>\n",
       "      <td>19</td>\n",
       "      <td>74</td>\n",
       "      <td>0.950000</td>\n",
       "      <td>AgamP3.chr2R</td>\n",
       "      <td>53</td>\n",
       "      <td>...</td>\n",
       "      <td>34</td>\n",
       "      <td>47760783</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E049926A;E049927A</td>\n",
       "      <td>AGAP004000</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP004000-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.950000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>345</th>\n",
       "      <td>345</td>\n",
       "      <td>259</td>\n",
       "      <td>21</td>\n",
       "      <td>3L</td>\n",
       "      <td>9810545</td>\n",
       "      <td>19</td>\n",
       "      <td>79</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>44</td>\n",
       "      <td>...</td>\n",
       "      <td>31</td>\n",
       "      <td>9810386</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E006174A;E006175A</td>\n",
       "      <td>AGAP010750</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP010750-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>354</th>\n",
       "      <td>354</td>\n",
       "      <td>322</td>\n",
       "      <td>21</td>\n",
       "      <td>3L</td>\n",
       "      <td>12733203</td>\n",
       "      <td>20</td>\n",
       "      <td>141</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>52</td>\n",
       "      <td>...</td>\n",
       "      <td>37</td>\n",
       "      <td>12733054</td>\n",
       "      <td>[{'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>E006860A;E006861A</td>\n",
       "      <td>AGAP010895</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP010895-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>355</th>\n",
       "      <td>355</td>\n",
       "      <td>288</td>\n",
       "      <td>20</td>\n",
       "      <td>3L</td>\n",
       "      <td>12881680</td>\n",
       "      <td>18</td>\n",
       "      <td>144</td>\n",
       "      <td>0.900000</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>36</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>12881545</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>E006921A;E006922A</td>\n",
       "      <td>AGAP010909</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP010909-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.900000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>387</th>\n",
       "      <td>387</td>\n",
       "      <td>204</td>\n",
       "      <td>20</td>\n",
       "      <td>3L</td>\n",
       "      <td>25198309</td>\n",
       "      <td>16</td>\n",
       "      <td>18</td>\n",
       "      <td>0.800000</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>38</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>25198162</td>\n",
       "      <td>[{'AgamP3', 'AaraD1', 'AgamM1', 'AquaS1', 'Aga...</td>\n",
       "      <td>E009091A;E009092A</td>\n",
       "      <td>AGAP011481</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP011481-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.800000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>401</th>\n",
       "      <td>401</td>\n",
       "      <td>367</td>\n",
       "      <td>19</td>\n",
       "      <td>3L</td>\n",
       "      <td>31964226</td>\n",
       "      <td>17</td>\n",
       "      <td>111</td>\n",
       "      <td>0.894737</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>49</td>\n",
       "      <td>...</td>\n",
       "      <td>29</td>\n",
       "      <td>31964092</td>\n",
       "      <td>[{'AaraD1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E009928A;E009929A</td>\n",
       "      <td>AGAP011712</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP011712-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.894737</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>411</th>\n",
       "      <td>411</td>\n",
       "      <td>327</td>\n",
       "      <td>21</td>\n",
       "      <td>3L</td>\n",
       "      <td>36310379</td>\n",
       "      <td>19</td>\n",
       "      <td>109</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3L</td>\n",
       "      <td>41</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>36310237</td>\n",
       "      <td>[{'AgamM1', 'AgamS1'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E010931A;E010932A;E010931B;E010932B</td>\n",
       "      <td>AGAP012014</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP012014-RA;AGAP012014-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>446</th>\n",
       "      <td>446</td>\n",
       "      <td>350</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>1517826</td>\n",
       "      <td>21</td>\n",
       "      <td>169</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>46</td>\n",
       "      <td>...</td>\n",
       "      <td>32</td>\n",
       "      <td>1517628</td>\n",
       "      <td>[]</td>\n",
       "      <td>E027585A;E027586A</td>\n",
       "      <td>AGAP007831</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP007831-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>463</th>\n",
       "      <td>463</td>\n",
       "      <td>422</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>4532621</td>\n",
       "      <td>20</td>\n",
       "      <td>160</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>42</td>\n",
       "      <td>...</td>\n",
       "      <td>28</td>\n",
       "      <td>4532422</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}]</td>\n",
       "      <td>E028459A;E028460A</td>\n",
       "      <td>AGAP008028</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008028-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>466</th>\n",
       "      <td>466</td>\n",
       "      <td>366</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>5111263</td>\n",
       "      <td>19</td>\n",
       "      <td>136</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>45</td>\n",
       "      <td>...</td>\n",
       "      <td>31</td>\n",
       "      <td>5111071</td>\n",
       "      <td>[{'AgamM1', 'AquaS1', 'AgamP3'}]</td>\n",
       "      <td>E028628A;E060594B;E028613B</td>\n",
       "      <td>AGAP008077</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008077-RA;AGAP008077-RB</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>476</th>\n",
       "      <td>476</td>\n",
       "      <td>250</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>8942164</td>\n",
       "      <td>20</td>\n",
       "      <td>134</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>43</td>\n",
       "      <td>...</td>\n",
       "      <td>33</td>\n",
       "      <td>8942048</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E029475B;E029476B;E029475A;E029476A</td>\n",
       "      <td>AGAP008317</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008317-RB;AGAP008317-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>504</th>\n",
       "      <td>504</td>\n",
       "      <td>239</td>\n",
       "      <td>19</td>\n",
       "      <td>3R</td>\n",
       "      <td>18667888</td>\n",
       "      <td>14</td>\n",
       "      <td>1</td>\n",
       "      <td>0.736842</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>37</td>\n",
       "      <td>...</td>\n",
       "      <td>23</td>\n",
       "      <td>18667697</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E031501A;E031502A</td>\n",
       "      <td>AGAP008823</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008823-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.736842</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>505</th>\n",
       "      <td>505</td>\n",
       "      <td>329</td>\n",
       "      <td>19</td>\n",
       "      <td>3R</td>\n",
       "      <td>18667978</td>\n",
       "      <td>14</td>\n",
       "      <td>2</td>\n",
       "      <td>0.736842</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>48</td>\n",
       "      <td>...</td>\n",
       "      <td>35</td>\n",
       "      <td>18667697</td>\n",
       "      <td>[{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...</td>\n",
       "      <td>E031501A;E031502A</td>\n",
       "      <td>AGAP008823</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008823-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.736842</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>518</th>\n",
       "      <td>518</td>\n",
       "      <td>389</td>\n",
       "      <td>20</td>\n",
       "      <td>3R</td>\n",
       "      <td>20821588</td>\n",
       "      <td>19</td>\n",
       "      <td>111</td>\n",
       "      <td>0.950000</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>40</td>\n",
       "      <td>...</td>\n",
       "      <td>24</td>\n",
       "      <td>20821414</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E031903A;E031904A</td>\n",
       "      <td>AGAP008919</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP008919-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.950000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>541</th>\n",
       "      <td>541</td>\n",
       "      <td>393</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>26419027</td>\n",
       "      <td>20</td>\n",
       "      <td>203</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>28</td>\n",
       "      <td>...</td>\n",
       "      <td>11</td>\n",
       "      <td>26418832</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E032758A;E032762A</td>\n",
       "      <td>AGAP009126</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP009126-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>566</th>\n",
       "      <td>566</td>\n",
       "      <td>313</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>36450394</td>\n",
       "      <td>19</td>\n",
       "      <td>160</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>39</td>\n",
       "      <td>...</td>\n",
       "      <td>26</td>\n",
       "      <td>36450247</td>\n",
       "      <td>[{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E034602A;E034603A</td>\n",
       "      <td>AGAP009577</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP009577-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>569</th>\n",
       "      <td>569</td>\n",
       "      <td>402</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>37790678</td>\n",
       "      <td>21</td>\n",
       "      <td>127</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>41</td>\n",
       "      <td>...</td>\n",
       "      <td>18</td>\n",
       "      <td>37790376</td>\n",
       "      <td>[]</td>\n",
       "      <td>E034991A;E034992A;E034993A</td>\n",
       "      <td>AGAP009664</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP009664-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>580</th>\n",
       "      <td>580</td>\n",
       "      <td>277</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>43854122</td>\n",
       "      <td>20</td>\n",
       "      <td>126</td>\n",
       "      <td>0.952381</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>47</td>\n",
       "      <td>...</td>\n",
       "      <td>37</td>\n",
       "      <td>43853955</td>\n",
       "      <td>[{'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E035772A;E035773A</td>\n",
       "      <td>AGAP009827</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP009827-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.952381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>584</th>\n",
       "      <td>584</td>\n",
       "      <td>290</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>44497504</td>\n",
       "      <td>19</td>\n",
       "      <td>93</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>56</td>\n",
       "      <td>...</td>\n",
       "      <td>45</td>\n",
       "      <td>44497356</td>\n",
       "      <td>[{'AquaS1', 'AgamS1'}, {'AsteI2', 'AsteS1'}]</td>\n",
       "      <td>E035919A;E035920A</td>\n",
       "      <td>AGAP009860</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP009860-RA</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>603</th>\n",
       "      <td>603</td>\n",
       "      <td>341</td>\n",
       "      <td>21</td>\n",
       "      <td>3R</td>\n",
       "      <td>49475758</td>\n",
       "      <td>19</td>\n",
       "      <td>185</td>\n",
       "      <td>0.904762</td>\n",
       "      <td>AgamP3.chr3R</td>\n",
       "      <td>30</td>\n",
       "      <td>...</td>\n",
       "      <td>16</td>\n",
       "      <td>49475523</td>\n",
       "      <td>[{'AgamM1', 'AgamP3', 'AgamS1'}]</td>\n",
       "      <td>E037194B;E037195B;E037194C;E037195C;E037194D;E...</td>\n",
       "      <td>AGAP010147</td>\n",
       "      <td>Yes</td>\n",
       "      <td>AGAP010147-RB;AGAP010147-RC;AGAP010147-RD;AGAP...</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>0.904762</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42 rows × 24 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Unnamed: 0  aligned_len  aligned_species chr       end  id_lineages  \\\n",
       "1             1          345               21  2L   2926735           18   \n",
       "33           33          298               21  2L  10356642           20   \n",
       "79           79          338               21  2L  26760891           20   \n",
       "85           85          322               21  2L  27674840           20   \n",
       "101         101          376               21  2L  34301269           20   \n",
       "118         118          488               20  2L  42393512           20   \n",
       "119         119          591               20  2L  42393789           20   \n",
       "120         120          291               20  2L  42542495           11   \n",
       "128         128          419               20  2L  45853080           19   \n",
       "133         133          283               21  2L  48612732           20   \n",
       "151         151          186               20  2R   3879160           12   \n",
       "152         152          324               20  2R   3879298           13   \n",
       "153         153          251               20  2R   3879298           12   \n",
       "183         183          311               21  2R   7053447           21   \n",
       "186         186          473               20  2R   8504834           18   \n",
       "189         189          408               21  2R  10593923           16   \n",
       "204         204          414               19  2R  16469958           18   \n",
       "211         211          324               21  2R  16889800           17   \n",
       "216         216          401               21  2R  20528316           20   \n",
       "231         231          353               21  2R  26654806           20   \n",
       "237         237          272               21  2R  27902640           20   \n",
       "269         269          281               20  2R  36019728           18   \n",
       "306         306          309               20  2R  47760981           19   \n",
       "345         345          259               21  3L   9810545           19   \n",
       "354         354          322               21  3L  12733203           20   \n",
       "355         355          288               20  3L  12881680           18   \n",
       "387         387          204               20  3L  25198309           16   \n",
       "401         401          367               19  3L  31964226           17   \n",
       "411         411          327               21  3L  36310379           19   \n",
       "446         446          350               21  3R   1517826           21   \n",
       "463         463          422               21  3R   4532621           20   \n",
       "466         466          366               21  3R   5111263           19   \n",
       "476         476          250               21  3R   8942164           20   \n",
       "504         504          239               19  3R  18667888           14   \n",
       "505         505          329               19  3R  18667978           14   \n",
       "518         518          389               20  3R  20821588           19   \n",
       "541         541          393               21  3R  26419027           20   \n",
       "566         566          313               21  3R  36450394           19   \n",
       "569         569          402               21  3R  37790678           21   \n",
       "580         580          277               21  3R  43854122           20   \n",
       "584         584          290               21  3R  44497504           19   \n",
       "603         603          341               21  3R  49475758           19   \n",
       "\n",
       "     indels  informativeness         seqid  snvs          ...           \\\n",
       "1        96         0.857143  AgamP3.chr2L    65          ...            \n",
       "33      139         0.952381  AgamP3.chr2L    38          ...            \n",
       "79      157         0.952381  AgamP3.chr2L    47          ...            \n",
       "85      178         0.952381  AgamP3.chr2L    35          ...            \n",
       "101     159         0.952381  AgamP3.chr2L    51          ...            \n",
       "118     137         1.000000  AgamP3.chr2L    65          ...            \n",
       "119     183         1.000000  AgamP3.chr2L    55          ...            \n",
       "120      17         0.550000  AgamP3.chr2L    30          ...            \n",
       "128     159         0.950000  AgamP3.chr2L    22          ...            \n",
       "133     149         0.952381  AgamP3.chr2L    27          ...            \n",
       "151       0         0.600000  AgamP3.chr2R    28          ...            \n",
       "152       0         0.650000  AgamP3.chr2R    50          ...            \n",
       "153       0         0.600000  AgamP3.chr2R    40          ...            \n",
       "183     135         1.000000  AgamP3.chr2R    36          ...            \n",
       "186      96         0.900000  AgamP3.chr2R    77          ...            \n",
       "189     169         0.761905  AgamP3.chr2R    43          ...            \n",
       "204     181         0.947368  AgamP3.chr2R    41          ...            \n",
       "211       3         0.809524  AgamP3.chr2R    56          ...            \n",
       "216     167         0.952381  AgamP3.chr2R    53          ...            \n",
       "231     145         0.952381  AgamP3.chr2R    49          ...            \n",
       "237     125         0.952381  AgamP3.chr2R    28          ...            \n",
       "269     119         0.900000  AgamP3.chr2R    49          ...            \n",
       "306      74         0.950000  AgamP3.chr2R    53          ...            \n",
       "345      79         0.904762  AgamP3.chr3L    44          ...            \n",
       "354     141         0.952381  AgamP3.chr3L    52          ...            \n",
       "355     144         0.900000  AgamP3.chr3L    36          ...            \n",
       "387      18         0.800000  AgamP3.chr3L    38          ...            \n",
       "401     111         0.894737  AgamP3.chr3L    49          ...            \n",
       "411     109         0.904762  AgamP3.chr3L    41          ...            \n",
       "446     169         1.000000  AgamP3.chr3R    46          ...            \n",
       "463     160         0.952381  AgamP3.chr3R    42          ...            \n",
       "466     136         0.904762  AgamP3.chr3R    45          ...            \n",
       "476     134         0.952381  AgamP3.chr3R    43          ...            \n",
       "504       1         0.736842  AgamP3.chr3R    37          ...            \n",
       "505       2         0.736842  AgamP3.chr3R    48          ...            \n",
       "518     111         0.950000  AgamP3.chr3R    40          ...            \n",
       "541     203         0.952381  AgamP3.chr3R    28          ...            \n",
       "566     160         0.904762  AgamP3.chr3R    39          ...            \n",
       "569     127         1.000000  AgamP3.chr3R    41          ...            \n",
       "580     126         0.952381  AgamP3.chr3R    47          ...            \n",
       "584      93         0.904762  AgamP3.chr3R    56          ...            \n",
       "603     185         0.904762  AgamP3.chr3R    30          ...            \n",
       "\n",
       "     target_snvs  target_start  \\\n",
       "1             52       2926537   \n",
       "33            24      10356481   \n",
       "79            40      26760778   \n",
       "85            20      27674693   \n",
       "101           32      34301104   \n",
       "118           47      42393238   \n",
       "119           29      42393509   \n",
       "120           12      42542260   \n",
       "128            6      45852918   \n",
       "133           16      48612544   \n",
       "151           16       3879042   \n",
       "152           34       3879042   \n",
       "153           26       3879096   \n",
       "183           21       7053270   \n",
       "186           49       8504608   \n",
       "189           20      10593690   \n",
       "204           38      16469779   \n",
       "211           39      16889615   \n",
       "216           42      20528121   \n",
       "231           36      26654601   \n",
       "237           21      27902493   \n",
       "269           37      36019603   \n",
       "306           34      47760783   \n",
       "345           31       9810386   \n",
       "354           37      12733054   \n",
       "355           29      12881545   \n",
       "387           26      25198162   \n",
       "401           29      31964092   \n",
       "411           22      36310237   \n",
       "446           32       1517628   \n",
       "463           28       4532422   \n",
       "466           31       5111071   \n",
       "476           33       8942048   \n",
       "504           23      18667697   \n",
       "505           35      18667697   \n",
       "518           24      20821414   \n",
       "541           11      26418832   \n",
       "566           26      36450247   \n",
       "569           18      37790376   \n",
       "580           37      43853955   \n",
       "584           45      44497356   \n",
       "603           16      49475523   \n",
       "\n",
       "                                          unid_species  \\\n",
       "1    [{'AgamM1', 'AaraD1', 'AgamP3'}, {'AsteI2', 'A...   \n",
       "33                              [{'AsteI2', 'AsteS1'}]   \n",
       "79                              [{'AgamM1', 'AgamP3'}]   \n",
       "85                              [{'AsteI2', 'AsteS1'}]   \n",
       "101                             [{'AsteI2', 'AsteS1'}]   \n",
       "118                                                 []   \n",
       "119                                                 []   \n",
       "120  [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aqu...   \n",
       "128                             [{'AsteI2', 'AsteS1'}]   \n",
       "133                             [{'AsteI2', 'AsteS1'}]   \n",
       "151  [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Afa...   \n",
       "152  [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "153  [{'AmelC1', 'AmerM1', 'AgamP3', 'AaraD1', 'Aga...   \n",
       "183                                                 []   \n",
       "186       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "189  [{'AgamM1', 'AaraD1', 'AgamP3'}, {'AmelC1', 'A...   \n",
       "204                             [{'AsteI2', 'AsteS1'}]   \n",
       "211  [{'AgamM1', 'AquaS1', 'AgamP3', 'AgamS1'}, {'A...   \n",
       "216                             [{'AsteI2', 'AsteS1'}]   \n",
       "231                             [{'AsteI2', 'AsteS1'}]   \n",
       "237                             [{'AsteI2', 'AsteS1'}]   \n",
       "269       [{'AgamP3', 'AgamS1'}, {'AsteI2', 'AsteS1'}]   \n",
       "306                             [{'AsteI2', 'AsteS1'}]   \n",
       "345       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "354                             [{'AgamP3', 'AgamS1'}]   \n",
       "355                   [{'AgamM1', 'AgamP3', 'AgamS1'}]   \n",
       "387  [{'AgamP3', 'AaraD1', 'AgamM1', 'AquaS1', 'Aga...   \n",
       "401       [{'AaraD1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "411       [{'AgamM1', 'AgamS1'}, {'AsteI2', 'AsteS1'}]   \n",
       "446                                                 []   \n",
       "463                             [{'AgamM1', 'AgamP3'}]   \n",
       "466                   [{'AgamM1', 'AquaS1', 'AgamP3'}]   \n",
       "476                             [{'AsteI2', 'AsteS1'}]   \n",
       "504  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "505  [{'AmelC1', 'AmerM1', 'AaraD1', 'AgamM1', 'Aga...   \n",
       "518                             [{'AsteI2', 'AsteS1'}]   \n",
       "541                             [{'AsteI2', 'AsteS1'}]   \n",
       "566       [{'AgamM1', 'AgamP3'}, {'AsteI2', 'AsteS1'}]   \n",
       "569                                                 []   \n",
       "580                             [{'AsteI2', 'AsteS1'}]   \n",
       "584       [{'AquaS1', 'AgamS1'}, {'AsteI2', 'AsteS1'}]   \n",
       "603                   [{'AgamM1', 'AgamP3', 'AgamS1'}]   \n",
       "\n",
       "                                                  exon        gene  intron  \\\n",
       "1                                    E014129A;E014130A  AGAP004734     Yes   \n",
       "33                                   E016098A;E016099A  AGAP005134     Yes   \n",
       "79   E020405C;E020406C;E020405B;E020406B;E020405A;E...  AGAP006107     Yes   \n",
       "85                 E020688A;E020689A;E020688B;E020689B  AGAP006176     Yes   \n",
       "101  E022297D;E022298D;E022297C;E022298C;E022297B;E...  AGAP006590     Yes   \n",
       "118                                  E024360A;E024361A  AGAP007086     Yes   \n",
       "119                                  E024361A;E024362A  AGAP007086     Yes   \n",
       "120                                  E024408A;E024409A  AGAP007092     Yes   \n",
       "128                E025379B;E025380B;E025379A;E025380A  AGAP007340     Yes   \n",
       "133  E026619C;E026620C;E026619D;E026620D;E026619A;E...  AGAP007643     Yes   \n",
       "151                         E039025A;E056936B;E053755B  AGAP001370     Yes   \n",
       "152                         E039025A;E056936B;E053755B  AGAP001370     Yes   \n",
       "153                         E039025A;E056936B;E053755B  AGAP001370     Yes   \n",
       "183                                  E040220A;E040221A  AGAP001632     Yes   \n",
       "186                E053266B;E040564B;E053266A;E040564A  AGAP001690     Yes   \n",
       "189                E041043B;E041044B;E041043A;E041044A  AGAP001799     Yes   \n",
       "204                E042394A;E042395A;E042394B;E042395B  AGAP002150     Yes   \n",
       "211                                  E042536A;E053752A  AGAP002172     Yes   \n",
       "216  E043230B;E043231B;E043230A;E043231A;E043230E;E...  AGAP002350     Yes   \n",
       "231                                  E044960A;E044962A  AGAP002748     Yes   \n",
       "237                E045221A;E045222A;E057892B;E045222B  AGAP002814     Yes   \n",
       "269                                  E047321A;E054664A  AGAP003327     Yes   \n",
       "306                                  E049926A;E049927A  AGAP004000     Yes   \n",
       "345                                  E006174A;E006175A  AGAP010750     Yes   \n",
       "354                                  E006860A;E006861A  AGAP010895     Yes   \n",
       "355                                  E006921A;E006922A  AGAP010909     Yes   \n",
       "387                                  E009091A;E009092A  AGAP011481     Yes   \n",
       "401                                  E009928A;E009929A  AGAP011712     Yes   \n",
       "411                E010931A;E010932A;E010931B;E010932B  AGAP012014     Yes   \n",
       "446                                  E027585A;E027586A  AGAP007831     Yes   \n",
       "463                                  E028459A;E028460A  AGAP008028     Yes   \n",
       "466                         E028628A;E060594B;E028613B  AGAP008077     Yes   \n",
       "476                E029475B;E029476B;E029475A;E029476A  AGAP008317     Yes   \n",
       "504                                  E031501A;E031502A  AGAP008823     Yes   \n",
       "505                                  E031501A;E031502A  AGAP008823     Yes   \n",
       "518                                  E031903A;E031904A  AGAP008919     Yes   \n",
       "541                                  E032758A;E032762A  AGAP009126     Yes   \n",
       "566                                  E034602A;E034603A  AGAP009577     Yes   \n",
       "569                         E034991A;E034992A;E034993A  AGAP009664     Yes   \n",
       "580                                  E035772A;E035773A  AGAP009827     Yes   \n",
       "584                                  E035919A;E035920A  AGAP009860     Yes   \n",
       "603  E037194B;E037195B;E037194C;E037195C;E037194D;E...  AGAP010147     Yes   \n",
       "\n",
       "                                                  mRNA repeat   utr  \\\n",
       "1                                        AGAP004734-RA   None  None   \n",
       "33                                       AGAP005134-RA   None  None   \n",
       "79           AGAP006107-RC;AGAP006107-RB;AGAP006107-RA   None  None   \n",
       "85                         AGAP006176-RA;AGAP006176-RB   None  None   \n",
       "101  AGAP006590-RD;AGAP006590-RC;AGAP006590-RB;AGAP...   None  None   \n",
       "118                                      AGAP007086-RA   None  None   \n",
       "119                                      AGAP007086-RA   None  None   \n",
       "120                                      AGAP007092-RA   None  None   \n",
       "128                        AGAP007340-RB;AGAP007340-RA   None  None   \n",
       "133  AGAP007643-RC;AGAP007643-RD;AGAP007643-RA;AGAP...   None   Yes   \n",
       "151                        AGAP001370-RA;AGAP001370-RB   None  None   \n",
       "152                        AGAP001370-RA;AGAP001370-RB   None  None   \n",
       "153                        AGAP001370-RA;AGAP001370-RB   None  None   \n",
       "183                                      AGAP001632-RA   None  None   \n",
       "186                        AGAP001690-RB;AGAP001690-RA   None  None   \n",
       "189                        AGAP001799-RB;AGAP001799-RA   None  None   \n",
       "204                        AGAP002150-RA;AGAP002150-RB   None  None   \n",
       "211                                      AGAP002172-RA   None  None   \n",
       "216  AGAP002350-RB;AGAP002350-RA;AGAP002350-RE;AGAP...   None  None   \n",
       "231                                      AGAP002748-RA   None  None   \n",
       "237                        AGAP002814-RA;AGAP002814-RB   None  None   \n",
       "269                                      AGAP003327-RA   None  None   \n",
       "306                                      AGAP004000-RA   None  None   \n",
       "345                                      AGAP010750-RA   None  None   \n",
       "354                                      AGAP010895-RA   None  None   \n",
       "355                                      AGAP010909-RA   None  None   \n",
       "387                                      AGAP011481-RA   None  None   \n",
       "401                                      AGAP011712-RA   None  None   \n",
       "411                        AGAP012014-RA;AGAP012014-RB   None  None   \n",
       "446                                      AGAP007831-RA   None  None   \n",
       "463                                      AGAP008028-RA   None  None   \n",
       "466                        AGAP008077-RA;AGAP008077-RB   None  None   \n",
       "476                        AGAP008317-RB;AGAP008317-RA   None  None   \n",
       "504                                      AGAP008823-RA   None  None   \n",
       "505                                      AGAP008823-RA   None  None   \n",
       "518                                      AGAP008919-RA   None  None   \n",
       "541                                      AGAP009126-RA   None  None   \n",
       "566                                      AGAP009577-RA   None  None   \n",
       "569                                      AGAP009664-RA   None  None   \n",
       "580                                      AGAP009827-RA   None  None   \n",
       "584                                      AGAP009860-RA   None  None   \n",
       "603  AGAP010147-RB;AGAP010147-RC;AGAP010147-RD;AGAP...   None  None   \n",
       "\n",
       "    id lineage proportion  \n",
       "1                0.857143  \n",
       "33               0.952381  \n",
       "79               0.952381  \n",
       "85               0.952381  \n",
       "101              0.952381  \n",
       "118              1.000000  \n",
       "119              1.000000  \n",
       "120              0.550000  \n",
       "128              0.950000  \n",
       "133              0.952381  \n",
       "151              0.600000  \n",
       "152              0.650000  \n",
       "153              0.600000  \n",
       "183              1.000000  \n",
       "186              0.900000  \n",
       "189              0.761905  \n",
       "204              0.947368  \n",
       "211              0.809524  \n",
       "216              0.952381  \n",
       "231              0.952381  \n",
       "237              0.952381  \n",
       "269              0.900000  \n",
       "306              0.950000  \n",
       "345              0.904762  \n",
       "354              0.952381  \n",
       "355              0.900000  \n",
       "387              0.800000  \n",
       "401              0.894737  \n",
       "411              0.904762  \n",
       "446              1.000000  \n",
       "463              0.952381  \n",
       "466              0.904762  \n",
       "476              0.952381  \n",
       "504              0.736842  \n",
       "505              0.736842  \n",
       "518              0.950000  \n",
       "541              0.952381  \n",
       "566              0.904762  \n",
       "569              1.000000  \n",
       "580              0.952381  \n",
       "584              0.904762  \n",
       "603              0.904762  \n",
       "\n",
       "[42 rows x 24 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# look at one of the introns\n",
    "meta = pd.read_csv(META_FILE)\n",
    "meta[meta['intron'] == 'Yes']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Query: 33 \n",
      "        Hit: 2L chromosome:AgamP3:2L:1:49364325:1\n",
      "Query range: [0:230] (1)\n",
      "  Hit range: [10356412:10356642] (1)\n",
      "Quick stats: evalue 2.9e-117; bitscore 425.85\n",
      "  Fragments: 1 (230 columns)\n",
      "     Query - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGG~~~AGCTG\n",
      "             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~|||||\n",
      "       Hit - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGG~~~AGCTG\n",
      "      Query: 33 \n",
      "        Hit: 2 dna:chromosome chromosome:AaegL5:2:1:474425716:1\n",
      "Query range: [0:71] (1)\n",
      "  Hit range: [204342875:204342946] (1)\n",
      "Quick stats: evalue 1.6e-25; bitscore 121.15\n",
      "  Fragments: 1 (71 columns)\n",
      "     Query - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGG~~~GTAAA\n",
      "             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~|||||\n",
      "       Hit - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGG~~~GTAAA\n",
      "      Query: 33 \n",
      "        Hit: supercont3.30 dna:supercontig supercontig:CpipJ2:supercont3.30:1...\n",
      "Query range: [0:68] (1)\n",
      "  Hit range: [1160152:1160220] (-1)\n",
      "Quick stats: evalue 7.2e-24; bitscore 115.61\n",
      "  Fragments: 1 (68 columns)\n",
      "     Query - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGG~~AAGGT\n",
      "             ||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||~~|||||\n",
      "       Hit - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGACGAGATGGTGGAGTTCTCGTCCGG~~AAGGT\n",
      "      Query: 33 \n",
      "        Hit: supercont3.30 dna:supercontig supercontig:CpipJ2:supercont3.30:1...\n",
      "Query range: [164:230] (1)\n",
      "  Hit range: [1160023:1160089] (-1)\n",
      "Quick stats: evalue 4.4e-21; bitscore 106.38\n",
      "  Fragments: 1 (66 columns)\n",
      "     Query - CAGGGCATGGCCCTTAACTTGGAGCCGGATAACGTCGGTGTGGTCGTGTTCGGTAACGACAAGCTG\n",
      "             ||||| |||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||\n",
      "       Hit - CAGGGTATGGCCCTTAACTTGGAGCCCGACAACGTCGGTGTGGTCGTGTTCGGTAACGACAAGCTG\n",
      "      Query: 33 \n",
      "        Hit: 2R dna_sm:chromosome chromosome:BDGP6:2R:1:25286936:1 REF\n",
      "Query range: [0:67] (1)\n",
      "  Hit range: [22800069:22800136] (1)\n",
      "Quick stats: evalue 1.2e-21; bitscore 108.23\n",
      "  Fragments: 1 (67 columns)\n",
      "     Query - GCCCGTGTGTACGGTCTGAAGAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGGACTTAAGG\n",
      "             |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||\n",
      "       Hit - GCCCGTGTCTACGGTCTGAACAACATCCAGGCCGATGAGATGGTGGAGTTCTCCTCCGGACTGAAGG\n"
     ]
    }
   ],
   "source": [
    "# example intron\n",
    "for hit in blast_qresult[33]:\n",
    "    for hsp in hit:\n",
    "        print(hsp)\n",
    "# two hits in Aaeg correspond to flanking exons (according to query range), other species don't have that"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'HSP' object has no attribute 'midline'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-13-a37115f974be>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      2\u001b[0m     \u001b[0;31m#print(hit)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mhsp\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mhit\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m             \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhsp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmidline\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'HSP' object has no attribute 'midline'"
     ]
    }
   ],
   "source": [
    "for hit in blast_qresult[33]:\n",
    "    #print(hit)\n",
    "    for hsp in hit:\n",
    "            print(hsp.midline)\n",
    "        \n",
    "print "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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