Question: Somatic Snp Mutation Igv Codon
1
gravatar for Hmm
8.6 years ago by
Hmm500
Hmm500 wrote:

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 • 2.3k views
ADD COMMENTlink modified 6.0 years ago by Biostar ♦♦ 20 • written 8.6 years ago by Hmm500
2
gravatar for Mitch Bekritsky
8.6 years ago by
Mitch Bekritsky1.2k
London, England
Mitch Bekritsky1.2k wrote:

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.

ADD COMMENTlink written 8.6 years ago by Mitch Bekritsky1.2k

Thank you..Youe explanation was really helpful!

ADD REPLYlink written 8.5 years ago by Hmm500

It was my pleasure!

ADD REPLYlink written 8.5 years ago by Mitch Bekritsky1.2k
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