Hi, I just wanted to know although the two quality scores have different formulae to calculate them, are they related to each other? I mean, can I say good MAPQ score implies the base qualities of the read is good?
Phred is 10 log10P where in Phred P is the probability of a miscalled base.
Samtools doesn't really support bit-scores or e-values akin to what you would see in a BLAST report. There is no sensical formula for mapping quality, since some reads map to multiple locations, others align poorly but that can be because of the read itself or SNPs. As the blog post shows, every tool rolls its own MAPQ.