IGV tutorial

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Inspecting SNPs, SNVs, and SVs

Homopolymer region with indel

Navigate to position chr21:19,518,412-19,518,497:

Center on the A within the homopolymer run (chr21:19,518,470):

Now color by read strand and sort alignments by base at the center. Note the poor base quality support in forward reads.

Center on the one base deletion (chr21:19,518,452):

Sort alignments by base, and notice the alternating insertions and deletions in reverse strand reads

Notes

The alternate allele is either a deletion or an insertion of one or two Ts.
The remaining bases are mismatched, because the alignment is now out of sync.
The dpSNP entry at this location (rs74604068) is an A->T, and in all likelihood an artifact.
i.e. the common variants from dbSNP include some cases that are actually common misalignments caused by repeats.