gsMapper contigs
 

Hello All,

What does the lower case and upper case Letters in the contigs build by gsMapper represent?

Also, How is HCDiff (high confidence) variations differences determined?

Thanks
HA

Hi Ha,

The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants that have at least 3 non-duplicate reads relative to the reference or to other reads at that specific location.

I also found another thread that discusses uppercase and lower case and maybe helpful.

http://seqanswers.com/forums/showthread.php?t=1948