Question: (Closed) Strange Alignment Issue
2
gravatar for Matt Shirley
4.9 years ago by
Matt Shirley7.9k
Cambridge, MA
Matt Shirley7.9k wrote:

I have encountered a strange issue in the alignment of a whole genome from Illumina. The below image shows PE reads mapped using Eland. Blue indicates base quality scores between 0-9 and white >=30. My question is this: What could possibly cause the drastic drop in base quality scores toward the 3' end of these reads to align in such an uncanny way? Does this look like and indel or translocation, or is this just the typical 5'->3' quality drop you would expect?

enter image description here

illumina mapping • 1.0k views
ADD COMMENTlink written 4.9 years ago by Matt Shirley7.9k
1

It looks like a GC rich region.

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum99k
1

... and high GC regions are problematic for Illumina (and others)

ADD REPLYlink written 4.9 years ago by JC6.2k

That makes sense. I was just searching for biological reasons that the base quality score would be drastically lower. I counted alleles using an awk one-liner and this region does have an elevated GC content in the reference. Thanks for the help.

ADD REPLYlink written 4.9 years ago by Matt Shirley7.9k
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