Dear samtools developers:
I have some questions about samtools pileup format
http://samtools.sourceforge.net/pileup.shtml:
1.
at the read base column, a symbol ^' marks the start of a read segment
which is a contiguous subsequence on the read separated byN/S/H' CIGAR
operations. The ASCII of the character following `^' minus 33 gives the
mapping quality.
The base that is the start of a read segment which is a contiguous
subsequence on the read separated by `N/S/H' CIGAR operations is before the
symbol '^' or after the symbol and the ASCII?
2.
A symbol `$' marks the end of a read segment.
The base that is the end of a read segment is before or after the symbol
'$'?
3.
For the insertions in the column of read bases, are the qualities of the
inserted bases given in the next column? What is the base of the read with
a insertion in the reference position? Where is the base quality of the
anchor base?
4.
For the deletions in the column of read bases, what is the base of the
read with a deletion in the reference position? Where is the base quality
of the anchor base?
I couldn't find the answers for the above questions. Could you please help
me with these problems? Thank you for your time!
Best
Jing
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