Hey guys, I went through pileup format specifications on the website many times, but still have some silly questions. Would you please give me some hints? Thanks!
One sentence in http://samtools.sourceforge.net/pileup.shtml says that "The ASCII of the character following `^' minus 33 gives the mapping quality." Take the first line as an example:
seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
This line shows that there are 24 reads covering this chromosome position on the reference, and the first base (^+.) in the last read matches the reference base at the same position with a "mapping quality" of 10 (43 - 33 = 10).
I have two questions:
1. Does "mapping quality" in the sentence "The ASCII of the character following `^' minus 33 gives the mapping quality" mean "mapping quality" of that read base, or "mapping quality" of the read containing that base?
2. Why this "mapping quality" is only available for the first read base (starting with ^), but not for all the other 23 read bases at the same position?
Sorry for the stupid questions because I really can't figure out those details.
Thanks in advance for any insights you will provide!
One sentence in http://samtools.sourceforge.net/pileup.shtml says that "The ASCII of the character following `^' minus 33 gives the mapping quality." Take the first line as an example:
seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&
This line shows that there are 24 reads covering this chromosome position on the reference, and the first base (^+.) in the last read matches the reference base at the same position with a "mapping quality" of 10 (43 - 33 = 10).
I have two questions:
1. Does "mapping quality" in the sentence "The ASCII of the character following `^' minus 33 gives the mapping quality" mean "mapping quality" of that read base, or "mapping quality" of the read containing that base?
2. Why this "mapping quality" is only available for the first read base (starting with ^), but not for all the other 23 read bases at the same position?
Sorry for the stupid questions because I really can't figure out those details.
Thanks in advance for any insights you will provide!
Comment