Hi Sung,
I am now off for weekend in Wells-next-the-Sea but to quickly answer your questions: to 1) Frank Wessely has come up with this table, so you need to ask him really. To 2) No, the BAM file does not store the AS, but it shouldn't be hard to get it to report it. To 3) The MAPQ value is calculated using the same algorithm that Bowtie 2 is using (or at least the Perl adaptation of the C code). More about this can be found further up here in the thread.
Cheers, Felix
I am now off for weekend in Wells-next-the-Sea but to quickly answer your questions: to 1) Frank Wessely has come up with this table, so you need to ask him really. To 2) No, the BAM file does not store the AS, but it shouldn't be hard to get it to report it. To 3) The MAPQ value is calculated using the same algorithm that Bowtie 2 is using (or at least the Perl adaptation of the C code). More about this can be found further up here in the thread.
Cheers, Felix
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