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Old 06-24-2015, 05:55 AM   #2
Jessica_L
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Location: Washington, D.C. metro area

Join Date: Feb 2010
Posts: 118
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I'm slowly picking up more data analysis and bioinformatics at work, so I've been doing some of the same kind of work lately. Here's how I would look at that:

I see 11 of the A and G reads, 9 of the C and T reads (along with some sequencing errors that are too probably too hard to call). Based on experience with Sanger data, it looks like a heterozygote, but IGV doesn't (as far as I know) really make it easy to see total read depth. To make that call, I'd look at something like the vcf file and check out the allele depth at the indicated SNPs to see how many reads you have of each genotype.

Since I'm still new at this, I'd be interested to see how others would analyze similar data.
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