454
Here is a example line of the SNP calling output, and what each section means:
0 3076 G A 0.0194% 15376/ 66 acc (335/ 8 rej): A: 3/ 0 ( 0/ 0) C: 5/ 0 ( 1/ 0) G: 15367/ 66 (334/ 8) T: 1/ 0 ( 0/ 0) iA: 0/ 0 iC: 0/ 0 iG: 0/ 0 iT: 0/ 0 Del: 0/0 F
0= reference number
3076= reference base (dash means deletion)
G= nucleotide in reference (dash means deletion)
A= nucleotide in sample (454 data)
0.0194%= percent of reads disagreeing with the reference
15376/ 66 acc= total forward/total reverse reads accepted
(335/ 8 rej):= total forward/total reverse reads rejected
A: 3/ 0 ( 0/ 0)= total forward reads calling A/ total reverese reads call A accepted (rejected reads calling A: fw/rc)
C: 5/ 0 ( 1/ 0)= same as above for C calls
G: 15367/ 66 (334/ 8)= same as above for G calls
T: 1/ 0 ( 0/ 0)= same as above for T calls
iA: 0/ 0= forward/reverse reads indicating an A inserted after this position
iC: 0/ 0= same as above for C insertions
iG: 0/ 0= same as above for G insertions
iT: 0/ 0= same as above for T insertions
Del: 0/0= forward/reverse reads indicating a deletion of this base
F= true or false. This is only informative if a truth file is given to the program
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Solid
# cov ref consen score confi F3 R3 score conf F3 R3 coord
94 C M 0.6002 0.9108 26/15 30/14 0.2598 0.8830 10/6 15/4 3429197
11 T Y 0.4650 0.9307 4/3 1/1 0.2736 0.9126 0/0 3/2 585338
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