[Samtools-help] Characters in pileup read bases field

[Benjamin K. <Ben...@ja...>]

Hello,

Is there a complete description of the possible characters in the read bases field created by samtools pileup?  I believe these are referred to as CIGAR strings.

There is a lot of useful information in the samtools manual page.  However, I can't decipher some of strings that I've generated including the following.


1.       What does the "^F" mean?

chr9    105019626       T       3       ,^F.^Fa @B7

chr9    105430949       A       8       ,,,....^F.      CCBBBBCB


2.       What does the ":" mean?

chr9    105001865       C       3       ,,^:.   17B


3.       What does the "~" mean?

chr1       120124682       N       T       39      0       60      4       TtT^~T  >BBA


4.       What does the "]" mean?

chr1       120124507       N       G       33      0       60      2       g^]g    @.


5.       What does the "!" mean?

chr1       120124333       N       A       4       0       0       1       ^!A     B


6.       What does the "?" mean?

chr1       120126381       N       G       33      0       30      2       G^?g    =1


7.       What does the "}" mean?

chr1       120125854       N       A       30      0       60      1       ^}A     A


Thank you,


-          Ben