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dfornika edited this page Apr 17, 2013
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BEGIN_COMMENT
CHROMAT_FILE: ca-21.s
ABI_THUMBPRINT: 056131235240000327232065337334
PHRED_VERSION: 0.990722.g
CALL_METHOD: phred
QUALITY_LEVELS: 99
TIME: Thu Apr 6 09:53:26 2000
TRACE_ARRAY_MIN_INDEX: 0
TRACE_ARRAY_MAX_INDEX: 9244
CHEM: prim
DYE: rhod
END_COMMENT
The DNA Block is delimited by the strings BEGIN_DNA
and END_DNA
. Each line of the block has three whitespace-delimited fields:
- The nucleotide identity {a,c,g,t}
- Phred-scaled quality score
- Trace array index
.
BEGIN_DNA
t 6 6
g 8 18
c 10 25
g 10 46
c 16 54
g 14 59
t 14 70
g 19 82
t 11 92
a 9 109
t 10 124
...
END_DNA
Tags can be added to .phd files to denote sequence features such as SNPs, primers, low complexity regions, etc. Below is a consed screenshot showing an alignment of several sequences, with tags that mark a C/T SNP at position 119.
BEGIN_TAG
TYPE: heterozygoteCT
SOURCE: polyPhred
UNPADDED_READ_POS: 98 98
DATE: 09/22/11 15:17:47
BEGIN_COMMENT
99
END_COMMENT
END_TAG