Hi all,
I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp single end and workflow is BWA-mem, GATK indel realignment, and visualization with the MATLAB NGS browser. There is a complete negative strand bias with a small island of positive strand bias, an 6pb segment of depth that is 5x normal for the rest of the genome (2300- vs 480-fold), nearly completely mapq 0, and distinct breakpoints. See the attached figure for a visualization.
Any ideas what kind of phenomenon could be causing this?
I'm seeing some very strange stuff with a resequenced prokaryotic genome coming from an Illumina HiSeq 2000. The design is 50bp single end and workflow is BWA-mem, GATK indel realignment, and visualization with the MATLAB NGS browser. There is a complete negative strand bias with a small island of positive strand bias, an 6pb segment of depth that is 5x normal for the rest of the genome (2300- vs 480-fold), nearly completely mapq 0, and distinct breakpoints. See the attached figure for a visualization.
Any ideas what kind of phenomenon could be causing this?
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