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FTL macros
========================================================================== -->
<!--==========================================================================
CSS styles
========================================================================== -->
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<!--==========================================================================
Index
========================================================================== -->
<center>
<div class="main">
<center> <h3> SnpEff: Variant analysis </h3> </center>
<div style="margin-left: .5em">
<table class="toc"><tr><td>
<center><b>Contents</b></center>
<a href="#summary">Summary</a><br>
<a href="#changeRateChr"> Variant rate by chromosome</a><br>
<a href="#changesByType">Variants by type</a><br>
<a href="#effectsImpact"> Number of variants by impact </a><br>
<a href="#effectsImpact"> Number of variants by functional class </a><br>
<a href="#effects"> Number of variants by effect </a><br>
<a href="#quality">Quality histogram</a><br>
<a href="#indels">InDel length histogram</a><br>
<a href="#baseChages">Base variant table</a><br>
<a href="#tstv">Transition vs transversions (ts/tv)</a><br>
<a href="#alleleFreq"> Allele frequency </a><br>
<a href="#alleleCount"> Allele Count </a><br>
<a href="#codonChanges"> Codon change table </a><br>
<a href="#aaChanges"> Amino acid change table </a><br>
<a href="#chrChanges"> Chromosome variants plots </a><br>
<a href="snpEff_genes.txt"> Details by gene </a><br>
</tr></td></table>
</div>
<!--==========================================================================
Summary table
========================================================================== -->
<hr>
<a name="summary">
<center>
<b>Summary</b><p>
<table border=0>
<tr bgcolor=ffffff>
<td valign=top> <b> Genome </b> </td>
<td> hg38 </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Date </b> </td>
<td> 2024-04-29 01:11 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> SnpEff version </b> </td>
<td> <pre>SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani</pre> </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Command line arguments </b> </td>
<td> <pre>SnpEff hg38 working_folder/results_bcf_cleaned/output_cleaned.vcf
</pre> </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Warnings </b> </td>
<td bgcolor="#ffff00"> 11,272 </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Errors </b> </td>
<td bgcolor="#dddddd"> 0 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Number of lines (input file) </b> </td>
<td> 76,656 </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Number of variants (before filter) </b> </td>
<td> 76,656 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Number of not variants <br>(i.e. reference equals alternative) </b> </td>
<td> 0 </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Number of variants processed <br> (i.e. after filter and non-variants) </b> </td>
<td> 76,656 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Number of known variants <br>(i.e. non-empty ID) </b> </td>
<td>
0
( 0% )
</td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Number of multi-allelic VCF entries <br>(i.e. more than two alleles) </b> </td>
<td>
0
</td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Number of effects </b> </td>
<td> 191,915 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Genome total length </b> </td>
<td> 3,247,448,939 </td>
</tr>
<tr bgcolor=dddddd>
<td valign=top> <b> Genome effective length </b> </td>
<td> 46,709,983 </td>
</tr>
<tr bgcolor=ffffff>
<td valign=top> <b> Variant rate </b> </td>
<td> 1 variant every 609 bases </td>
</tr>
</table>
<p>
</center>
<!--==========================================================================
Variant rate by chromosome
========================================================================== -->
<hr>
<a name="changeRateChr">
<center>
<b> Variants rate details </b><p>
<table border=1>
<tr><th> Chromosome </th><th> Length </th><th> Variants </th><th> Variants rate </th></tr>
<tr>
<td> 21 </td>
<td class="numeric"> 46,709,983 </td>
<td class="numeric"> 76,656 </td>
<td class="numeric"> 609 </td>
</tr>
<tr>
<th> Total </th>
<th class="numeric"> 46,709,983 </th>
<th class="numeric"> 76,656 </th>
<th class="numeric"> 609 </th>
</tr>
</table>
</center>
<!--==========================================================================
Variants by type
========================================================================== -->
<hr>
<a name="changesByType">
<center>
<b> Number variants by type</b><p>
<table border=1>
<thead>
<tr>
<th> <b> Type </b> </th>
<th> <b> Total </b> </th>
</tr>
</thead>
<tbody>
<tr>
<td> <b> SNP </b> </td>
<td class="numeric" bgcolor="#ff0000"> 66,426 </td>
</tr>
<tr>
<td> <b> MNP </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
<tr>
<td> <b> INS </b> </td>
<td class="numeric" bgcolor="#00ff00"> 4,651 </td>
</tr>
<tr>
<td> <b> DEL </b> </td>
<td class="numeric" bgcolor="#03fb00"> 5,579 </td>
</tr>
<tr>
<td> <b> MIXED </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
<tr>
<td> <b> INV </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
<tr>
<td> <b> DUP </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
<tr>
<td> <b> BND </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
<tr>
<td> <b> INTERVAL </b> </td>
<td class="numeric" bgcolor="ffffff"> 0 </td>
</tr>
</tbody>
<tfoot>
<tr>
<th><b>Total </b> </th>
<th class="numeric"> 76,656 </th>
</tr>
</tfoot>
</table>
</center>
<!--==========================================================================
Effects by impact
========================================================================== -->
<hr>
<a name="effectsImpact">
<center>
<b> Number of effects by impact </b> <p>
<table border=0>
<thead>
<tr>
<th><b> Type (alphabetical order) </b></th>
<th> </th>
<th> Count </th>
<th> Percent </th>
</tr>
</thead>
<tr>
<td> <b> HIGH </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00ff00"> 41 </td>
<td class="numeric" bgcolor="#00ff00"> 0.021% </td>
</tr>
<tr>
<td> <b> LOW </b> </td>
<th> </th>
<td class="numeric" bgcolor="#01fd00"> 1,109 </td>
<td class="numeric" bgcolor="#01fd00"> 0.578% </td>
</tr>
<tr>
<td> <b> MODERATE </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 744 </td>
<td class="numeric" bgcolor="#00fe00"> 0.388% </td>
</tr>
<tr>
<td> <b> MODIFIER </b> </td>
<th> </th>
<td class="numeric" bgcolor="#ff0000"> 190,021 </td>
<td class="numeric" bgcolor="#ff0000"> 99.013% </td>
</tr>
</table><br>
<p>
</center>
<!--==========================================================================
Effects by functional class
========================================================================== -->
<hr>
<a name="effectsFuncClass">
<center>
<b> Number of effects by functional class </b> <p>
<table border=0>
<thead>
<tr>
<th><b> Type (alphabetical order) </b></th>
<th> </th>
<th> Count </th>
<th> Percent </th>
</tr>
</thead>
<tr>
<td> <b> MISSENSE </b> </td>
<th> </th>
<td class="numeric" bgcolor="#e41a00"> 722 </td>
<td class="numeric" bgcolor="#e41a00"> 47.036% </td>
</tr>
<tr>
<td> <b> NONSENSE </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00ff00"> 10 </td>
<td class="numeric" bgcolor="#00ff00"> 0.651% </td>
</tr>
<tr>
<td> <b> SILENT </b> </td>
<th> </th>
<td class="numeric" bgcolor="#ff0000"> 803 </td>
<td class="numeric" bgcolor="#ff0000"> 52.313% </td>
</tr>
</table><br>
<p>
Missense / Silent ratio: 0.8991
</center>
<!--==========================================================================
Effects stats
========================================================================== -->
<hr>
<a name="effects">
<center>
<b> Number of effects by type and region </b> <p>
<table border=0>
<tr>
<th> Type </th>
<th> Region </th>
</tr>
<tr>
<td> <table border=0>
<thead>
<tr>
<th><b> Type (alphabetical order) </b></th>
<th> </th>
<th> Count </th>
<th> Percent </th>
</tr>
</thead>
<tr>
<td> <b> 3_prime_UTR_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#04fa00"> 1,984 </td>
<td class="numeric" bgcolor="#04fa00"> 1.032% </td>
</tr>
<tr>
<td> <b> 5_prime_UTR_premature_start_codon_gain_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 31 </td>
<td class="numeric" bgcolor="#00fe00"> 0.016% </td>
</tr>
<tr>
<td> <b> 5_prime_UTR_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 247 </td>
<td class="numeric" bgcolor="#00fe00"> 0.128% </td>
</tr>
<tr>
<td> <b> conservative_inframe_deletion </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00ff00"> 1 </td>
<td class="numeric" bgcolor="#00ff00"> 0.001% </td>
</tr>
<tr>
<td> <b> conservative_inframe_insertion </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 2 </td>
<td class="numeric" bgcolor="#00fe00"> 0.001% </td>
</tr>
<tr>
<td> <b> disruptive_inframe_deletion </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 8 </td>
<td class="numeric" bgcolor="#00fe00"> 0.004% </td>
</tr>
<tr>
<td> <b> disruptive_inframe_insertion </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 11 </td>
<td class="numeric" bgcolor="#00fe00"> 0.006% </td>
</tr>
<tr>
<td> <b> downstream_gene_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#14ea00"> 10,001 </td>
<td class="numeric" bgcolor="#14ea00"> 5.202% </td>
</tr>
<tr>
<td> <b> frameshift_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 12 </td>
<td class="numeric" bgcolor="#00fe00"> 0.006% </td>
</tr>
<tr>
<td> <b> intergenic_region </b> </td>
<th> </th>
<td class="numeric" bgcolor="#5ea000"> 45,862 </td>
<td class="numeric" bgcolor="#5ea000"> 23.857% </td>
</tr>
<tr>
<td> <b> intron_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#ff0000"> 123,676 </td>
<td class="numeric" bgcolor="#ff0000"> 64.334% </td>
</tr>
<tr>
<td> <b> missense_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#01fd00"> 722 </td>
<td class="numeric" bgcolor="#01fd00"> 0.376% </td>
</tr>
<tr>
<td> <b> non_coding_transcript_exon_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#01fd00"> 908 </td>
<td class="numeric" bgcolor="#01fd00"> 0.472% </td>
</tr>
<tr>
<td> <b> splice_acceptor_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 11 </td>
<td class="numeric" bgcolor="#00fe00"> 0.006% </td>
</tr>
<tr>
<td> <b> splice_donor_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 9 </td>
<td class="numeric" bgcolor="#00fe00"> 0.005% </td>
</tr>
<tr>
<td> <b> splice_region_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 311 </td>
<td class="numeric" bgcolor="#00fe00"> 0.162% </td>
</tr>
<tr>
<td> <b> stop_gained </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 10 </td>
<td class="numeric" bgcolor="#00fe00"> 0.005% </td>
</tr>
<tr>
<td> <b> synonymous_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#01fd00"> 803 </td>
<td class="numeric" bgcolor="#01fd00"> 0.418% </td>
</tr>
<tr>
<td> <b> upstream_gene_variant </b> </td>
<th> </th>
<td class="numeric" bgcolor="#0fef00"> 7,631 </td>
<td class="numeric" bgcolor="#0fef00"> 3.97% </td>
</tr>
</table><br>
</td>
<td> <table border=0>
<thead>
<tr>
<th><b> Type (alphabetical order) </b></th>
<th> </th>
<th> Count </th>
<th> Percent </th>
</tr>
</thead>
<tr>
<td> <b> DOWNSTREAM </b> </td>
<th> </th>
<td class="numeric" bgcolor="#14ea00"> 10,001 </td>
<td class="numeric" bgcolor="#14ea00"> 5.211% </td>
</tr>
<tr>
<td> <b> EXON </b> </td>
<th> </th>
<td class="numeric" bgcolor="#05f900"> 2,454 </td>
<td class="numeric" bgcolor="#05f900"> 1.279% </td>
</tr>
<tr>
<td> <b> INTERGENIC </b> </td>
<th> </th>
<td class="numeric" bgcolor="#5ea000"> 45,862 </td>
<td class="numeric" bgcolor="#5ea000"> 23.897% </td>
</tr>
<tr>
<td> <b> INTRON </b> </td>
<th> </th>
<td class="numeric" bgcolor="#ff0000"> 123,395 </td>
<td class="numeric" bgcolor="#ff0000"> 64.297% </td>
</tr>
<tr>
<td> <b> SPLICE_SITE_ACCEPTOR </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 11 </td>
<td class="numeric" bgcolor="#00fe00"> 0.006% </td>
</tr>
<tr>
<td> <b> SPLICE_SITE_DONOR </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00ff00"> 8 </td>
<td class="numeric" bgcolor="#00ff00"> 0.004% </td>
</tr>
<tr>
<td> <b> SPLICE_SITE_REGION </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 291 </td>
<td class="numeric" bgcolor="#00fe00"> 0.152% </td>
</tr>
<tr>
<td> <b> UPSTREAM </b> </td>
<th> </th>
<td class="numeric" bgcolor="#0fef00"> 7,631 </td>
<td class="numeric" bgcolor="#0fef00"> 3.976% </td>
</tr>
<tr>
<td> <b> UTR_3_PRIME </b> </td>
<th> </th>
<td class="numeric" bgcolor="#04fa00"> 1,984 </td>
<td class="numeric" bgcolor="#04fa00"> 1.034% </td>
</tr>
<tr>
<td> <b> UTR_5_PRIME </b> </td>
<th> </th>
<td class="numeric" bgcolor="#00fe00"> 278 </td>
<td class="numeric" bgcolor="#00fe00"> 0.145% </td>
</tr>
</table><br>
</td>
</tr>
</table>
<p>
<img src="http://chart.apis.google.com/chart?cht=bvs&chs=800x300&chbh=50,4,8&chxt=y,y,x,x&chtt=Variations&chxp=1,50.0|3,50.0&chxr=0,0.0,64.29669384883933|1,0.0,100.0|3,0.0,100.0&chco=00FFFF,FA8072,FF0000,A52A2A,FFA500,DEB887,E9967A,7FFFD4,808080&chdl=Upstream|5%27UTR|Exon|Splice+Donor|Intron|Splice+Acceptor|3%27UTR|Downstream|Intergenic&chxl=1:|%25|2:|Intergenic|Up|5%27UTR|Exon|Donor|Intron|Acceptor|Exon|3%27UTR|Down|Intergenic|3:|&chd=e:AAD9AAAAAAAAAAAAAAAAAA,AAAAAJAAAAAAAAAAAAAAAA,AAAAAABRAAAAAABRAAAAAA,AAAAAAAAAAAAAAAAAAAAAA,AAAAAAAAAA..AAAAAAAAAA,AAAAAAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAABCAAAA,AAAAAAAAAAAAAAAAAAFMAA,XyAAAAAAAAAAAAAAAAAAXy" border=1><p>
</center>
<!--==========================================================================
Quality
========================================================================== -->
<hr>
<a name="quality">
<b> Quality:</b>
<p>
<pre>
<table class="histo">
<tr> <th width=15%>Min</th><td>20</td> </tr>
<tr> <th>Max</th><td>2,784</td> </tr>
<tr> <th>Mean</th><td>170.28</td> </tr>
<tr> <th>Median</th><td>102</td> </tr>
<tr> <th>Standard deviation</th><td>240.756</td> </tr>
<tr> <th>Values</th><td>20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,902,903,905,906,907,908,909,910,911,913,914,915,916,917,918,919,920,921,922,923,924,925,926,928,929,930,931,932,933,934,935,937,938,939,940,941,942,943,944,945,946,947,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,969,970,971,973,974,975,976,977,978,979,981,983,984,985,986,987,989,990,991,994,995,996,997,998,1000,1002,1003,1004,1006,1007,1008,1009,1010,1011,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1027,1028,1029,1030,1031,1032,1033,1035,1036,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1052,1054,1055,1056,1057,1058,1059,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1076,1077,1078,1080,1081,1084,1087,1088,1089,1090,1091,1092,1093,1095,1096,1097,1098,1099,1100,1101,1102,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1119,1120,1121,1122,1123,1125,1126,1127,1128,1129,1131,1132,1134,1136,1137,1141,1142,1143,1144,1145,1147,1148,1149,1150,1151,1152,1153,1155,1158,1159,1160,1161,1163,1164,1165,1166,1167,1168,1170,1171,1172,1173,1174,1175,1177,1178,1179,1180,1181,1184,1185,1187,1188,1189,1190,1191,1192,1193,1194,1195,1198,1199,1200,1201,1203,1204,1207,1209,1210,1211,1212,1213,1214,1215,1217,1218,1219,1220,1222,1224,1225,1227,1229,1230,1232,1233,1234,1236,1237,1238,1240,1242,1244,1245,1247,1248,1252,1253,1254,1255,1256,1258,1260,1261,1262,1263,1266,1267,1268,1269,1270,1271,1275,1276,1277,1280,1281,1282,1283,1284,1285,1286,1292,1293,1294,1295,1296,1297,1298,1299,1300,1303,1304,1305,1306,1309,1311,1312,1313,1314,1316,1320,1321,1322,1323,1328,1329,1330,1332,1333,1335,1336,1337,1338,1341,1344,1345,1346,1351,1352,1353,1354,1355,1357,1358,1359,1360,1362,1363,1364,1365,1367,1368,1369,1371,1372,1373,1374,1376,1378,1381,1383,1384,1385,1386,1387,1388,1390,1392,1393,1394,1395,1397,1398,1399,1400,1404,1405,1406,1408,1409,1410,1411,1412,1415,1417,1418,1419,1420,1424,1425,1426,1427,1429,1430,1431,1433,1436,1437,1438,1439,1440,1441,1444,1446,1447,1448,1449,1450,1451,1453,1454,1455,1456,1458,1459,1461,1462,1463,1467,1468,1469,1473,1474,1476,1477,1478,1479,1480,1481,1482,1485,1486,1487,1491,1493,1494,1496,1498,1499,1501,1502,1504,1505,1507,1511,1513,1516,1517,1520,1521,1522,1530,1531,1534,1535,1536,1537,1538,1543,1544,1545,1548,1550,1554,1563,1567,1568,1569,1570,1572,1573,1574,1576,1578,1581,1582,1585,1589,1591,1592,1593,1594,1595,1596,1598,1600,1603,1604,1606,1608,1609,1610,1612,1615,1617,1619,1623,1626,1627,1628,1632,1636,1637,1638,1639,1640,1641,1642,1645,1647,1649,1651,1652,1654,1655,1661,1662,1663,1664,1665,1666,1667,1671,1673,1674,1675,1676,1677,1679,1682,1683,1686,1689,1691,1692,1695,1696,1698,1703,1704,1707,1709,1711,1714,1715,1716,1717,1719,1722,1723,1725,1727,1729,1730,1732,1736,1737,1738,1740,1743,1744,1746,1747,1748,1749,1751,1752,1755,1757,1759,1762,1764,1765,1766,1767,1769,1770,1771,1773,1776,1777,1778,1782,1784,1785,1788,1789,1790,1791,1792,1801,1805,1807,1815,1816,1817,1819,1820,1821,1823,1824,1828,1829,1830,1831,1834,1835,1841,1842,1845,1846,1850,1851,1853,1856,1859,1862,1864,1867,1869,1873,1875,1879,1884,1886,1887,1889,1891,1892,1893,1900,1901,1903,1905,1907,1913,1916,1918,1925,1927,1931,1934,1936,1937,1938,1940,1941,1947,1948,1950,1953,1955,1957,1958,1962,1963,1964,1965,1967,1968,1970,1971,1972,1973,1988,1989,1991,1995,1997,2000,2004,2012,2015,2016,2024,2025,2027,2029,2031,2040,2046,2047,2053,2054,2058,2062,2065,2067,2079,2081,2084,2089,2092,2093,2097,2099,2102,2104,2105,2107,2109,2111,2112,2119,2122,2126,2129,2130,2132,2137,2138,2142,2147,2150,2151,2152,2165,2168,2169,2170,2174,2178,2179,2189,2192,2193,2195,2197,2201,2203,2206,2209,2211,2213,2214,2217,2220,2221,2223,2225,2227,2232,2238,2245,2250,2257,2259,2260,2266,2272,2278,2280,2286,2293,2294,2295,2303,2304,2306,2309,2311,2313,2316,2317,2318,2321,2328,2334,2337,2353,2355,2356,2361,2363,2366,2378,2380,2381,2389,2391,2398,2405,2406,2409,2410,2419,2421,2423,2427,2428,2433,2438,2439,2441,2443,2449,2450,2453,2457,2458,2459,2460,2462,2464,2466,2469,2473,2478,2479,2480,2481,2482,2483,2484,2486,2488,2499,2543,2554,2573,2575,2580,2583,2584,2585,2587,2595,2598,2599,2602,2610,2613,2614,2620,2622,2627,2629,2644,2647,2650,2651,2657,2661,2670,2672,2679,2680,2682,2690,2691,2693,2695,2696,2702,2705,2710,2719,2720,2725,2730,2736,2737,2739,2743,2744,2745,2747,2752,2757,2765,2766,2770,2776,2781,2782,2783,2784</td> </tr>
<tr> <th>Count</th><td>1178,1226,1153,1091,952,817,841,831,805,684,733,625,592,551,532,504,592,471,460,443,463,428,654,489,441,476,487,482,476,443,446,462,416,457,468,434,405,385,428,433,410,360,388,392,422,390,356,360,362,451,343,337,372,379,352,449,352,346,302,343,314,350,297,315,294,328,312,290,287,303,276,324,256,283,272,275,296,314,244,273,264,279,340,265,229,248,291,269,302,248,239,250,240,253,246,251,244,250,241,212,207,238,253,231,245,193,215,253,223,220,233,201,191,218,190,261,219,192,198,204,186,223,199,194,198,217,189,167,167,153,174,227,173,191,168,155,190,205,144,177,170,164,209,185,133,169,180,178,178,164,162,150,157,159,174,151,168,171,163,144,133,126,138,133,167,142,140,164,144,158,156,141,146,126,123,131,136,112,130,143,154,144,143,114,140,139,109,137,124,114,120,124,124,144,120,97,197,145,112,128,115,106,101,111,92,110,115,102,119,124,106,96,95,111,90,98,88,98,90,92,97,93,112,102,82,106,88,93,86,95,103,94,76,91,101,82,92,80,88,98,89,102,91,89,98,85,85,78,96,78,78,76,68,70,75,82,75,75,86,58,58,72,56,75,58,86,70,66,74,71,61,80,65,63,70,60,52,53,57,60,66,61,57,52,52,51,53,69,66,56,65,52,54,52,63,53,63,73,49,58,49,51,60,35,48,48,42,44,58,39,49,50,51,40,57,42,49,55,47,58,30,55,54,34,44,51,36,36,42,35,32,49,36,49,37,35,48,37,35,46,24,35,43,37,37,50,41,43,23,35,46,34,26,25,42,29,39,42,23,36,36,41,45,27,42,28,20,31,40,26,27,44,37,24,32,32,28,30,33,37,29,35,24,30,28,27,26,21,29,26,27,30,23,34,37,31,22,38,33,25,26,24,25,25,23,32,20,35,21,20,20,20,35,14,22,29,26,24,20,23,21,21,25,24,23,26,15,18,21,21,16,23,21,18,26,24,19,24,18,25,15,19,43,20,17,24,24,17,18,14,22,15,14,21,17,20,14,18,20,10,13,17,13,13,12,14,14,22,14,13,18,13,11,16,14,15,20,11,12,15,12,15,10,17,13,17,13,19,12,12,18,7,14,11,17,8,10,5,5,8,10,11,10,23,13,11,6,7,13,12,9,6,9,10,10,8,9,17,9,9,7,14,8,6,13,9,8,16,16,8,13,7,10,12,15,5,11,11,12,9,11,12,8,6,5,9,15,15,10,11,8,14,12,14,6,11,10,10,10,4,7,6,6,4,9,9,6,12,5,5,8,6,8,11,6,7,12,7,10,7,7,8,12,10,8,7,10,5,8,7,3,10,4,6,9,9,9,11,7,4,3,9,7,8,10,5,11,6,2,7,4,7,7,4,4,5,4,5,7,5,6,7,2,4,4,3,6,11,8,10,5,3,8,3,5,1,7,6,5,9,5,6,5,5,1,8,1,8,7,4,4,4,8,5,3,4,8,9,6,2,7,6,4,10,3,5,4,7,6,6,5,2,4,3,5,6,6,7,6,4,4,11,9,1,2,6,8,5,1,9,10,4,5,4,2,4,5,2,2,5,5,5,7,3,1,2,3,2,1,2,5,4,5,3,3,4,2,4,1,5,2,4,5,3,4,3,5,1,3,1,5,6,3,3,2,7,10,2,4,7,2,6,6,4,1,6,4,5,5,1,1,3,5,2,3,4,1,3,5,1,3,5,2,3,4,4,3,5,4,4,1,3,4,4,2,4,2,1,3,4,4,3,3,2,4,6,2,4,2,2,7,3,2,1,4,2,3,6,3,3,1,4,2,5,1,2,5,5,4,3,3,2,2,1,2,5,2,5,5,2,3,2,3,5,1,3,5,3,2,1,1,3,2,3,3,2,4,4,4,4,2,3,2,4,4,2,5,1,4,2,2,1,2,1,5,2,5,4,3,2,4,3,2,2,2,2,1,3,1,1,1,3,1,3,2,3,3,3,2,4,4,2,5,2,4,5,6,2,3,3,1,4,3,2,4,1,1,2,2,2,4,1,3,4,2,3,3,2,4,2,2,1,1,1,3,2,6,2,3,2,5,1,7,4,3,3,2,2,2,2,2,12,1,1,2,1,3,5,2,4,2,1,1,2,1,1,3,3,2,1,1,6,2,2,3,3,2,1,2,3,1,3,2,2,1,3,2,2,3,1,1,2,1,2,1,1,1,3,1,3,1,1,1,2,1,3,2,1,4,3,1,3,2,1,4,5,6,2,1,2,2,2,1,2,2,2,1,4,1,1,3,2,3,1,2,3,1,1,2,2,1,2,3,4,1,1,1,1,1,3,3,3,1,3,2,1,2,3,2,2,2,4,1,2,1,2,2,1,2,2,2,1,4,1,1,2,3,1,2,3,1,1,1,2,2,2,4,1,2,1,1,4,1,3,1,1,1,3,2,2,1,1,1,3,5,2,1,1,4,1,1,1,1,3,2,1,2,3,4,1,1,2,1,2,1,2,2,1,2,1,2,1,2,4,4,1,2,3,1,1,2,2,1,2,1,1,5,1,1,1,1,2,1,3,3,2,1,2,2,1,1,2,1,2,2,2,1,3,1,1,2,1,1,1,1,2,1,1,1,2,1,2,3,2,3,1,1,1,1,2,2,1,2,2,2,1,1,1,1,2,2,1,2,2,1,1,1,1,1,2,2,2,1,3,1,1,1,1,4,1,1,2,1,1,2,1,3,1,3,1,1,1,1,1,1,1,1,2,1,1,4,1,1,2,3,2,4,1,1,1,1,1,1,2,1,1,2,1,2,1,2,1,3,2,1,1,1,1,1,1,1,1,2,2,1,3,1,2,1,1,2,2,1,1,3,1,2,1,1,1,2,1,1,2,2,1,1,1,3,1,2,1,2,1,1,1,3,1,2,3,1,1,3,4,2,2,1,1,1,1,2,2,1,1,1,1,1,1,1,4,2,1,3,1,1,1,1,1,1,1,1,3,1,1,1,2,1,1,2,1,1,1,1,3,1,1,1,1,1,3,1,1,2,1,1,1,2,1,1,1,1,2,1,2,1,1,1,1,2,2,3,2,2,1,1,1,1,2,1,1,1,2,1,1,3,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,3,3,1,1,1,1,2,1,1,1,4,2,1,2,1,1,1,2,1,2,1,1,2,2,2,1,1,2,1,1,1,2,1,1,2,1,1,1,1,2,1,1,1,2,1,1,2,1,1,1,2,2,1,2,1,2,1,3,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,1,2,1,3,1,1,2,1,2,2,1,1,1,1,1,1,1,2,1,1,1,1,3,1,2,1,1,2,1,1,1,2,1,1,1,1,1,1,2,1,1,1,1,2,1,1,1,2,3,5,1,1,2,1,1,1,1,4,1,1,2,1,1,2,1,1,2,1,1,1,2,1,2,1,1,1,1,2,1,1,2,1,1,1,1,1,1,1,1,2,1,1,1,1,2,2,1,2,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,1,3,1,1,1,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,3,2,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,4,3,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,2,2,1,3,1,1,1,1,1,1,1,1,1,1,1,2,2,1,3,1,3,1,3,1,1,1,1,7,7</td> </tr>
</tr>
</table>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chg=275.0,641.0,3,2&chtt=Quality+histogram&chxr=0,5.0,6417.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Count|2:|22||||||||||||||||||||||||||||||198||||||||||||||||||||||||||||||374||||||||||||||||||||||||||||||550||||||||||||||||||||||||||||||728||||||||||||||||||||||||||||||908||||||||||||||||||||||||||||||1115||||||||||||||||||||||||||||||1370||||||||||||||||||||||||||||||1680||||||||||||||||||||||||||||||2123|||||||||||||||||||||||||||||2781|3:|Quality&chd=e:..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"><br>
</pre>
<!--==========================================================================
InDels
========================================================================== -->
<hr>
<a name="indels">
<b> Insertions and deletions length:</b>
<p>
<pre>
<table class="histo">
<tr> <th width=15%>Min</th><td>0</td> </tr>
<tr> <th>Max</th><td>18</td> </tr>
<tr> <th>Mean</th><td>1.108</td> </tr>
<tr> <th>Median</th><td>1</td> </tr>
<tr> <th>Standard deviation</th><td>1.408</td> </tr>
<tr> <th>Values</th><td>0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18</td> </tr>
<tr> <th>Count</th><td>2474,6516,325,472,155,109,29,59,13,19,14,17,7,6,5,1,4,2,3</td> </tr>
</tr>
</table>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chg=1.0,651.0,3,2&chxp=1,50.0|3,50.0&chtt=Insertion+deletion+length+histogram&chxr=0,1.0,6516.0|1,0.0,100.0|3,0.0,100.0&chd=e:Xr..CkEfBSApAAAAAAAAAAAAAAAAAAAAAAAAAA&chxl=1:|Count|2:|0||||||||||10||||||||18|3:|Length"><br>
</pre>
<!--==========================================================================
Base changes
========================================================================== -->
<hr>
<a name="baseChages">
<center>
<b> Base changes (SNPs) </b> <p>
<table border=1>
<tr>
<td> </td> <th> <b> A </b> </th> <th> <b> C </b> </th> <th> <b> G </b> </th> <th> <b> T </b> </th>
</tr>
<tr> <th> <b> A </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="#07f700"> 2,710 </td><td class="numeric" bgcolor="#d72700"> 10,125 </td><td class="numeric" bgcolor="#00ff00"> 2,453 </td> </tr>
<tr> <th> <b> C </b> </th><td class="numeric" bgcolor="#2ad400"> 3,957 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="#09f500"> 2,775 </td><td class="numeric" bgcolor="#ff0000"> 11,514 </td> </tr>
<tr> <th> <b> G </b> </th><td class="numeric" bgcolor="#f20c00"> 11,057 </td><td class="numeric" bgcolor="#07f700"> 2,729 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="#25d900"> 3,788 </td> </tr>
<tr> <th> <b> T </b> </th><td class="numeric" bgcolor="#00ff00"> 2,453 </td><td class="numeric" bgcolor="#db2300"> 10,255 </td><td class="numeric" bgcolor="#04fa00"> 2,610 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr>
</table>
</center>
<p>
<!--==========================================================================
Ts/Tv
========================================================================== -->
<hr>
<a name="tstv">
<center> <b> Ts/Tv (transitions / transversions) </b> <p> </center>
<small>
<b>Note:</b> Only SNPs are used for this statistic.<br>
<b>Note:</b> This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
</small>
<p>
<center>
<table border=1>
<tr> <th> Transitions </th><td class="numeric"> 216,160 </td> </tr>
<tr> <th> Transversions </th><td class="numeric"> 108,181 </td> </tr>
<tr> <th> Ts/Tv ratio </th><td class="numeric"> 1.9981 </td> </tr>
</table>
</center>
<p>
<b>All variants:</b>
<pre>Sample ,working_folder/results_bwa/HG00109.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00119.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00129.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00139.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00149.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00159.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00239.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00249.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00259.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG01789.GRCh38DH.exome.chr21.bam,working_folder/results_bwa/HG00099.GRCh38DH.exome.chr21.bam,Total
Transitions ,18837,40300,7346,12263,7321,39859,40284,14814,15407,12161,7568,216160
Transversions ,9223,20619,3337,6024,3417,20212,21065,7220,7592,5831,3641,108181
Ts/Tv ,2.042,1.955,2.201,2.036,2.143,1.972,1.912,2.052,2.029,2.086,2.079,1.998
</pre>
<p>
<b>Only known variants</b> (i.e. the ones having a non-empty ID field):
<pre>No results available (empty input?)</pre>
<p>
<!--==========================================================================
Allele frequency
========================================================================== -->
<hr>
<a name="alleleFreq">
<center> <b> Allele frequency </b> <p> </center>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chg=10.0,1174.0,3,2&chtt=Allele+Frequency+%25&chxr=0,51.0,11796.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Count|2:|0||||||||||13||||||||||28||||||||||42||||||||||59||||||||||71||||||||||87||||||||100|3:|Alleles+frequency&chd=e:DNDNCkCkD2HrBSOFBSSkBSEfApXrD2LhEfB7cKBSDNKPB7QACkAAK4AAFxB7ApAAAAApXrAAAAAAApBSAAD2AAIUAAApAAK4ApFxBSApR7AABSFxApQpBSAAK4AAGaCkApAAAAAA.."><br>
<table class="histo">
<tr> <th width=15%>Min</th><td>0</td> </tr>
<tr> <th>Max</th><td>100</td> </tr>
<tr> <th>Mean</th><td>50.022</td> </tr>
<tr> <th>Median</th><td>41</td> </tr>
<tr> <th>Standard deviation</th><td>32.977</td> </tr>
<tr> <th>Values</th><td>0,4,5,6,7,8,9,10,11,12,13,14,15,16,18,20,21,22,25,27,28,30,31,33,35,36,37,38,40,41,42,43,44,45,50,54,55,56,57,58,59,60,61,62,63,64,65,66,68,70,71,72,75,77,78,80,81,83,85,86,87,88,90,91,92,93,94,95,100</td> </tr>
<tr> <th>Count</th><td>702,654,549,530,857,1483,390,2704,307,3469,294,977,189,4492,844,2282,957,467,5234,346,702,1944,517,3088,548,133,2070,113,1205,480,264,138,68,169,4510,86,69,89,182,370,69,818,83,1595,60,274,51,2125,252,1175,344,171,3451,154,340,1112,241,3127,347,55,2071,56,1285,590,280,148,58,56,11796</td> </tr>
</tr>
</table>
<p>
<!--==========================================================================
Allele Count
========================================================================== -->
<hr>
<a name="alleleCount">
<center> <b> Allele Count </b> <p> </center>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chtt=Allele+Count&chg=2.0,1297.0,3,2&chxp=1,50.0|3,50.0&chxr=0,30.0,13009.0|1,0.0,100.0|3,0.0,100.0&chd=e:DN..8JutoUczhRTNXCLhOuGaHCCkDNBSBSApApAAAAAAAA&chxl=1:|Count|2:|0||||||||||10||||||||||20||22|3:|Allele+Count"><br>
<table class="histo">
<tr> <th width=15%>Min</th><td>0</td> </tr>
<tr> <th>Max</th><td>22</td> </tr>
<tr> <th>Mean</th><td>4.769</td> </tr>
<tr> <th>Median</th><td>4</td> </tr>
<tr> <th>Standard deviation</th><td>3.617</td> </tr>
<tr> <th>Values</th><td>0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22</td> </tr>
<tr> <th>Count</th><td>702,13009,12270,9634,8301,5973,6831,4008,4762,2375,3040,1354,1569,652,769,348,389,164,188,81,96,30,111</td> </tr>
</tr>
</table>
<p>
<!--==========================================================================
Hom/Het table
========================================================================== -->
<hr>
<a name="homHet">
<center> <b> Hom/Het per sample </b> <p> </center>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chg=1.0,1955.0,3,2&chxp=1,50.0|3,50.0&chtt=Heterozygous+genotypes&chd=e:R78yAAIUAA7g..NcOuIUAp&chxr=0,3632.0,23189.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Heterozygous+count|2:|0||||||||||10|3:|Sample+number"><br>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chg=1.0,1920.0,3,2&chxp=1,50.0|3,50.0&chd=e:Xr..AAK4AA-t-tOuQAI9Ap&chtt=Homozygous+%28ALT%29+genotypes&chxr=0,4016.0,23224.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Homozygous+count|2:|0||||||||||10|3:|Sample+number"><br>
<img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chg=1.0,5415.0,3,2&chxp=1,50.0|3,50.0&chtt=Missing+genotypes&chd=e:mZAA..z1.WB7AAtbsz1H-E&chxr=0,7813.0,61968.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Missing+count|2:|0||||||||||10|3:|Sample+number"><br>
<pre>Sample_names , working_folder/results_bwa/HG00109.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00119.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00129.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00139.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00149.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00159.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00239.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00249.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00259.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG01789.GRCh38DH.exome.chr21.bam, working_folder/results_bwa/HG00099.GRCh38DH.exome.chr21.bam
Reference , 15353, 22907, 6965, 11373, 7280, 22321, 22686, 13492, 13439, 10738, 7673
Het , 9217, 22258, 3632, 6188, 3806, 22006, 23189, 7913, 8199, 6344, 3886
Hom , 11252, 23224, 4091, 7343, 4016, 22856, 22968, 8599, 8980, 6785, 4339
Missing , 40834, 8267, 61968, 51752, 61554, 9473, 7813, 46652, 46038, 52789, 60758
</pre>
<p>
<!--==========================================================================
Codon change table
========================================================================== -->
<hr>
<a name="codonChanges">
<center>
<b> Codon changes</b> <p>
<div class="note">
How to read this table: <br>
- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.<br>
- Red background colors indicate that more changes happened (heat-map).<br>
- Diagonals are indicated using grey background color <br>
- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).<br>
<p>
</div><p>
<table border=1>
<thead>
<tr>
<th> </th>
<th> - </th> <th> AAA </th> <th> AAC </th> <th> AAG </th> <th> AAT </th> <th> ACA </th> <th> ACC </th> <th> ACG </th> <th> ACT </th> <th> AGA </th> <th> AGC </th> <th> AGG </th> <th> AGT </th> <th> ATA </th> <th> ATC </th> <th> ATG </th> <th> ATT </th> <th> CAA </th> <th> CAC </th> <th> CAG </th> <th> CAT </th> <th> CCA </th> <th> CCC </th> <th> CCG </th> <th> CCT </th> <th> CGA </th> <th> CGC </th> <th> CGG </th> <th> CGT </th> <th> CTA </th> <th> CTC </th> <th> CTG </th> <th> CTT </th> <th> GAA </th> <th> GAC </th> <th> GAG </th> <th> GAT </th> <th> GCA </th> <th> GCC </th> <th> GCG </th> <th> GCT </th> <th> GGA </th> <th> GGC </th> <th> GGG </th> <th> GGT </th> <th> GTA </th> <th> GTC </th> <th> GTG </th> <th> GTT </th> <th> TAC </th> <th> TAT </th> <th> TCA </th> <th> TCC </th> <th> TCG </th> <th> TCT </th> <th> TGA </th> <th> TGC </th> <th> TGG </th> <th> TGT </th> <th> TTA </th> <th> TTC </th> <th> TTG </th> <th> TTT </th>
</tr>
</thead>
<tr>
<th> - </th>
<th class="numeric">   </th>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#06f800"> 2 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#06f800"> 2 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#1ae400"> 5 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#20de00"> 6 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
</tr>
<tr>
<th> AAA </th>
<td class="numeric" bgcolor="ffffff">   </td>
<th class="numeric">   </th>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#1ae400"> 5 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="#897500"> 22 </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>
<td class="numeric" bgcolor="ffffff">   </td>