I ran reformat.sh on a SAM file and the log seemed fine:

Input is being processed as unpaired
Input:                      35583 reads             52857642 bases
Output:                     35583 reads (100.00%)   52857642 bases (100.00%)

But then in the results, the sum of the all matched bases across all Phred scores (95,085,736bp) exceeds the total number of bases aligned in my SAM file (52,857,642bp).

#Quality    Match   Sub Ins Del
0   0   0   0   0
1   0   0   0   0
…   …   …   …   …
40  2350122 634 2   14
41  92735614    15774   188 626

TOTAL 95085736 16408 190 640

So I was wondering how we're supposed to interpret these statistics?

I'm interested in quantifying the proportion of matched, mismatched, deleted and inserted bases from all my alignments. Is reformat.sh qahist the appropriate tool to use?

I hope Brian Bushnell sees this. I read through the BBMap documentation but couldn't find an explanation.