I am hoping to estimate the proportion of mismatches, insertions, and deletions to a reference sequence in a BAM file. I applied the picard CollectAlignmentSummaryMetrics tool, and I find that all of my reads pass filtering, 2477324592 total bases are aligned, and I have a PF_MISMATCH_RATE of 0.000348. However, when I instead sum all of the "NM" tags for all alignments, then divide by the total number of aligned bases, I calculate a higher mismatch rate of 0.0008732263. I similarly overestimate if I try to get the total number of indels from the MD tags, then compare to PF_INDEL_RATE. Could someone explain the discrepancy here? Thanks for your help.
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