What does the following Mapping Quality Score even mean?
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?
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