After reading the documentation at https://github.com/genome/bam-readcount/blob/master/README.textile there is one column in the output from bam-readcount that I still don't understand.
Columns 1-4 are chromosome, position, reference base, readcount. Columns 6-9 are colon separated values reflecting counts and quality metrics for reads with A, C, G, T, and ambiguous calls at the current position.
But what is column 5? In my output, it begins with an "=", then every colon separated value is "0" in each row.
Here is a sample row:
1 897037 C 27 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:25:51.36:30.44:35.72:12:13:0.44:0.01:8.20:13:0.41:74.48:0.51 G:2:60.00:32.50:37.00:1:1:0.58:0.01:32.50:1:0.24:76.00:0.28 T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
Thank you very much.