Mr./Ms. ,

I checked the count distributions from *_dis files, and compared the numbers with the read counts from BAM files. For a specific MSI locus, I thought that the sum of the number of count distribution equal to the total reads from the BAM files. I checked the read count through IGV, but found that the sum of the number from *_dis files always less than the total read count from BAM files through IGV. So I'm wondering is there any filtration process when counting the read count?

For example:

the MONO27 MSI site
chr2 39573062 GTCTC 27[A] GAGTG
T: 0 0 0 0 0 0 0 0 0 0 0 16 34 104 263 434 639 674 507 293 104 18 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

The sum of the count is 3091, however, the total reads is 3896 at the start of the MONO27 site and 4341 at the end of the site, using IGV.

Look forward to your reply, thanks.