[Samtools-help] CollectAlignmentSummaryMetrics error rates

[Richard C. <rco...@bc...>]

Hi all,

Does anyone know how these numbers are calculated? ie, are they based on 
flags, the cigar, or sequence string?

PF_MISMATCH_RATE 0.47867 0.476719 0.477708
PF_HQ_ERROR_RATE 0.48216 0.481005 0.481589
PF_INDEL_RATE 0.00009 0.000095 0.000093

Also, a question about interpretation...  is this telling me that .477 
percent of my aligned bases are mismatch errors?

thanks,
RIchard