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2.9 years ago
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I'm trying to find the mapping quality scores for bam files specifically for my gene of interest. Using the following code
samtools view Aligned.sortedByCoord.out.bam 2:132052355-132117013| awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}'
Mean MAPQ = 220.236
I got a MAPQ of 220.236. The score is confusing me and I would love if an expert to explain what is happening. I had previously been told that 60 was the highest?
