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Strange Alignment Issue

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
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written by Matt Shirley Matt Shirley

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

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written by JC JC

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.

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written by Matt Shirley Matt Shirley

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