IGV tutorial

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Inspecting SNPs, SNVs, and SVs

Two neighbouring SNPs

In this section we will be looking in detail at 8 positions in the genome, and determining whether they represent real events or artifacts.

Navigate to region chr21:19,479,237-19,479,814:

Note two heterozygous variants, one corresponds to a known dbSNP (G/T on the right) the other does not (C/T on the left).

Zoom in and center on the C/T SNV on the left:

Sort alignments by base: right-click on a center base and choose Sort by base.

Color alignments by read strand: click the track gear icon on the right and choose Color by read strand.

Notes

Reads have high base quality scores except one (where the alt allele is the last base of the read). Note that igv.js dims the color of a base if it has low quality.
Reads have good mapping qualities, show no strand bias, and the allele frequency is consistent with a heterozygous mutation.

Question

How does Color by read strand help?