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Comment Block

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

DNA Block

The DNA Block is delimited by the strings BEGIN_DNA and END_DNA. Each line of the block has three whitespace-delimited fields:

  1. The nucleotide identity {a,c,g,t}
  2. Phred-scaled quality score
  3. 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

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.

consed screenshot

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
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