Fastq quality string, quality

Question

[vascoambrogi]

I began reading into a fastq file of reads around 130 bp of my whole genome sequencing.

What caught my eye were the quality string of each read.

At first I was pretty happy, each nucleotide, with some rare exceptions, achieves a quality score of ‘F’ which is very good.

Then I got suspicious, can it be possible to have a persistent ‘F’ score for each nucleotide, with some sparse ‘:’ score?

And there does not seem to be nothing in between, its wether I get a ‘F’ or rarely I get an ‘:’.

[Ram]

Run your FASTQ through fastqc. Eyeballing it won't help.