Hi,

I am trying to count all the bases found at a specific site within a bam file using the following command:

samtools mpileup -Ef reference.fa  -r chr2:200-200 aln.bam

This produces the following output:

chr2   200    C    2130    .$.$.$.$..,,,,$............,.........T.....................,.,,,,,,.,.........................................................................A...............................,,.*...*.................,,,,,*............A*.........................................................................*..................................................................................................................................................,*,,,.....,......,.....,..................................................................,.,..*,.,,..*.,*,,,,................,........,..................,.......*...................,,,,,.,,,,,*..................................................,.,,,,,,.,,*,,,.,,,,...............,.......................................................T...............................................................,...........,.,.........,..,,*,,,.,,,,,..................................,.A...................................................................................................................................................,..................................,...............................................,...,.............,..,...,,,......,............,....,.......................................................................,,,,.,,,,,,,...........,..................,*..,,,,,,.,.............................................................,................,...........................................A.....................................................................,..,,..*,,,,,................,,............,..,...................,.........,,,,,.,,.,.........................................................................................................................................,............................,................,............,.,.,,,......,,,,,,,,,,,,,,,,,,........................,,..,............,.,,......,,,.,,,,,,,,,.........,.,,,,,,,,,,,,.,,,,,,.,,............................,,,,,,,,,.,,,,,,,,,,,,,...........T.........,......,......^~.^~.^R.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^>,^~.^\.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~,^~.^~.^~.^~.^~.^~,^~.^~.^~.^~.^_.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.^[.^~.^~.^~.^~.^~.^~.^~.^b.^~.^~.^~.^=,^~.^~.^~.^~.^~.^~.^~.^~.^~.^~,^~.^~.^~.^~.^P,^~.^~.^~.^~.^X.^~.^~.^>.^~.^~.^~.^~.^~.^~.^~.^~.^~.^~.

I realize that A,T correspond to alternate alleles and that . and , correspond to the reference allele depending on strand but what do all the other symbols correspond to?

Cheers, Joseph