View Single Post
Old 06-11-2017, 09:31 AM   #13
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 123
Default

ok. thank you for the link.
I have one more question to the output file of BBmap.
This is an output file:
Code:
Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                  99,7746%         2365043        99,8117%         1168097245
unambiguous:             96,5758%         2289219        96,6551%         1131155596
ambiguous:                3,1988%           75824         3,1566%           36941649
low-Q discards:           0,0000%               0         0,0000%                  0

perfect best site:       36,0494%          854511        36,4545%          426626981
semiperfect site:        36,0505%          854537        36,4556%          426639736

Match Rate:                   NA               NA        99,5357%         1166772129
Error Rate:              63,8415%         1510509         0,4634%            5431521
Sub Rate:                13,2884%          314407         0,0677%             794173
Del Rate:                56,8578%         1345272         0,3512%            4117267
Ins Rate:                15,1778%          359111         0,0444%             520081
N Rate:                   0,0128%             302         0,0009%              10862

Average coverage:                       96,08
Standard deviation:                     26,28
Percent scaffolds with any coverage:    100,00
Percent of reference bases covered:     99,28
can you explain me "perfect best site" and "semiperfect site"
and
if "pct reads" is the percent of mapped reads. are there "num reads" are the number of mapped reads? because if t'is the number of mapped reads i haven't 2365043 reads?

and why the Error rate for "pct reads" is high?
thanks for your help.

Last edited by mido1951; 06-11-2017 at 09:34 AM.
mido1951 is offline   Reply With Quote