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Somatic Snp Mutation Igv Codon

I am looking at a tumor/normal pair illumina HiSeq data paired end. When i open my normal and tumor bam files in IGV, i expect to see a mutation at a specific location(which i do see). But the base there is A. The mutation is suppose to change G -> T but what the reads show me only is A -> C and on the Reference sequence in IGV i see a "C" (so that is fine). How can I explain this to someone?

The codon i am looking at is "ACC" so the complement of that is "TGG"..right...why don't i see any T and G in my reads? Why are there only A and C?

somatic snp
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updated by Biostar Biostar • written by Hmm • Hmm

1 answer

This may not generally be the case, but when I use BWA to align reads, it reports aligned reads relative to the original genome you used for alignment (i.e. the forward strands of all the chromosomes). Therefore, if a read maps to the reverse strand of a chromosome, BWA will report the reverse complement of the read you originally submitted as the sequence after alignment in the SAM/BAM file.

If your coding sequence is on the reverse strand of the original genome you used for alignment, then it will only report G->T, not A->C, since that is what the sequence was aligned to.

To double check, look for your gene in the genome browser. If it is transcribed from the reverse strand, then that could be why it's reporting the G->T substitution.

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written by Mitch Bekritsky Mitch Bekritsky

Thank you..Youe explanation was really helpful!

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written by Hmm • Hmm

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