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.