Uneven base quality in NGS read?
I am analyzing the NGS data from my colleage. AFAK, it is a 16s amplicon data from illumina's novaseq 6000.
The quality's report from fastp has a really weird quality distribution. While overall (mean) quality is good, the quality of each base is uneven with a huge spurious huge drop all over sequence (see pic below). Is this normal?
Thank you.
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what's the region size sequenced? v1 and v6 are small regions.
They are 250/250 pair-reads. Reverse reads 's quality look similar to forward but worse.