Weird FastQC per base quality graph

Question

[alexmartsink]

For some reason I'm only getting one bar at position 1, everything else has no yellow bars. Everything else seems mostly fine, apart form per base sequence content which for some reason has alot of variability early on.

[GenoMax]

There may be a lot of N calls at first base position. You could check some of the reads. These should be handled by the aligner at the time of alignment and likely will cause no issues.

[cpad0112]

either you can use trim-n or filter by quality with cutadapt or in this case, you can trim first base from all the reads.. Positions with Ns have low quality.