I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error.
wgsim -e 0 -r 0 sequence.fa seq_0_1.fq seq_0_2.fq
To my knowledge, this is a perfect simulation. Next, I give the paired alignments to bwa for alignment.
bwa mem -M sequence.fa seq_0_1.fq seq_0_2.fq > P0.sam
Now, I check the ASCII of base quality (column 11 in the SAM format, the specification is here).
head -n 3 P0.sam | cut -f11 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
According to this page, the ASCII (in order of quality) is:
Question: My experiment is supposed to be perfect, so my base-quality metrics are expected to appear near the right-end of the list (like x,y,z). However, my metric I is no-where near the top of the list. In particular, I'm unable to achieve anything from J to ~. Why?