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Fastqc Shows A Weird Kmer Distribution

I ran FatsQC on a set of 4 Illumina PE exomes and got really weird graphs for the kmer distribution. I've never seen this pattern before - does anyone know what is going on and what to do about it?

kmer distribution

kmer distribution

kmer distribution

enter image description here

illumina fastqc
• 4,117 views • link
written by Nick Nick

2 answers

Those k-mers almost perfectly correspond to the TruSeq adapter sequence. Was there anything peculiar that showed up in the overrepresented sequences table?

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written by kelvin.c.chan • kelvin.c.chan

You are right - there are TruSeq adaptors among the overrepresented sequences. I'll remove them and then re-run fastqc.

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written by Nick Nick

@kelvin.c.chan: I did remove the over-represented sequences for one of the samples and the graph changed somewhat but there are still peaks (see below) although fastqc no longer reports any over-represented sequences. Any ideas? kmer distribution

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written by Nick Nick

How did you remove the TruSeq-containing sequences?

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written by bow bow

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