hello, I have assembled paired reads with Megahit, and now I want to know how many reads are uesd to make up those contigs(reads%).
I have tried bbmap and find this in STR:
Pairing data: pct reads num reads pct bases num bases
mated pairs: 36.1655% 52614378 37.2210% 15687793904
bad pairs: 2.9658% 4314738 3.0270% 1275797796
insert size avg: 338.64
Read 1 data: pct reads num reads pct bases num bases
mapped: 46.8503% 68158783 46.8339% 10145704082
unambiguous: 46.3132% 67377420 46.2987% 10029749277
ambiguous: 0.5371% 781363 0.5353% 115954805
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 18.9679% 27594901 19.0008% 4116175782
semiperfect site: 21.5567% 31361110 21.5960% 4678380777
rescued: 0.7859% 1143367
Match Rate: NA NA 95.8928% 9735647890
Error Rate: 41.6441% 36902108 2.0807% 211247627
Sub Rate: 41.6137% 36875119 1.9638% 199375874
Del Rate: 0.7019% 622010 0.0682% 6927772
Ins Rate: 0.8580% 760297 0.0487% 4943981
N Rate: 6.7397% 5972234 2.0264% 205736337
(read2 data omitted)
Average coverage: 305.47
Standard deviation: 902.02
Percent scaffolds with any coverage: 100.00
Percent of reference bases covered: 99.95
And I wonder what does this means?
How to calculate the reads% mapped to contigs?
Thanks.
(new to this ,question may be stupid but I have no idea about this.)
I have tried bbmap and find this in STR:
Pairing data: pct reads num reads pct bases num bases
mated pairs: 36.1655% 52614378 37.2210% 15687793904
bad pairs: 2.9658% 4314738 3.0270% 1275797796
insert size avg: 338.64
Read 1 data: pct reads num reads pct bases num bases
mapped: 46.8503% 68158783 46.8339% 10145704082
unambiguous: 46.3132% 67377420 46.2987% 10029749277
ambiguous: 0.5371% 781363 0.5353% 115954805
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 18.9679% 27594901 19.0008% 4116175782
semiperfect site: 21.5567% 31361110 21.5960% 4678380777
rescued: 0.7859% 1143367
Match Rate: NA NA 95.8928% 9735647890
Error Rate: 41.6441% 36902108 2.0807% 211247627
Sub Rate: 41.6137% 36875119 1.9638% 199375874
Del Rate: 0.7019% 622010 0.0682% 6927772
Ins Rate: 0.8580% 760297 0.0487% 4943981
N Rate: 6.7397% 5972234 2.0264% 205736337
(read2 data omitted)
Average coverage: 305.47
Standard deviation: 902.02
Percent scaffolds with any coverage: 100.00
Percent of reference bases covered: 99.95
And I wonder what does this means?
How to calculate the reads% mapped to contigs?
Thanks.
(new to this ,question may be stupid but I have no idea about this.)
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