Hi,
I am a newbie of SAM tools. And right now I am using function of "pileup" in SAMtools to identify SNPs in my deep sequencing data. The output is like that.
I know the meaning of all the other columns except the ones for column 4, 5, 6, 7. I suspect column 4 tells the mismatch situation between reference genome and my reads, but I don't know why there are letters out of "A/T/G/C". For column 5, 6, and 7, are they some scores? I am not sure. Could someone provide any information about that? Thanks a lot!
I am a newbie of SAM tools. And right now I am using function of "pileup" in SAMtools to identify SNPs in my deep sequencing data. The output is like that.
chr1 9155441 G T 21 221 60 8 TttttTTT ;KJOLLJJ
chr1 9162037 A G 9 40 60 9 gGGGGGGGG !B91,0,,!
chr1 9163797 G R 1 1 60 7 ,.A,,.. eeRedgg
chr1 9174351 C S 0 11 60 1 g J
chr1 9162037 A G 9 40 60 9 gGGGGGGGG !B91,0,,!
chr1 9163797 G R 1 1 60 7 ,.A,,.. eeRedgg
chr1 9174351 C S 0 11 60 1 g J
I know the meaning of all the other columns except the ones for column 4, 5, 6, 7. I suspect column 4 tells the mismatch situation between reference genome and my reads, but I don't know why there are letters out of "A/T/G/C". For column 5, 6, and 7, are they some scores? I am not sure. Could someone provide any information about that? Thanks a lot!
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