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Old 10-17-2017, 07:08 AM   #1
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Default Strange GC patterns in FastQC results

Hi there

I wonder if anyone has seen similar patterns in genomic Illumina reads before, or have any idea of what is causing this?

So these are genomic reads from an eukaryote, produced by standard DNA isolation, prepared using Truseq v4 and sequenced paired-end on an Ilumina Hiseq 2000 machine.
The quality of the reads are generally good, but the 'sequence content across all bases', produced by FastQC, seem strange. These are the R1 reads, but I see the exact same pattern in the R2 reads.

Little is known about the genome as there exists no reference. But could this pattern be a result of high abundance of certain repeats in the genome?
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