how to count the mapped reads with bbmap?

[GUZUMO]

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.)

[GenoMax]

Just to clarify. You took the original reads and then mapped them back to the assembly done with MegaHit using BBMap?

[GUZUMO]

yes,is there something wrong?
thx

[Brian Bushnell]

For paired reads, you can find the total percent mapped by adding the read 1 percent (where it says "mapped: 46.8503%") and read 2 percent, then dividing by 2. The different columns tell you the count/percent of each event. For example, for the "num bases" column and "sub rate" row, the entry indicates there were 199375874 base substitutions (mismatches) compared to the reference, for read 1.

[GUZUMO]

Thanks,
So how to understand "Match Rate" and "Error Rate"?
is there a pdf or something that explain the result of bbmap?

[Brian Bushnell]

Considering the cigar strings from alignment, "Match Rate" is the number of symbols indicating a reference match (=) and error rate is the number indicating substitution, insertion, or deletion (X, I, D).

BBMap does not have a PDF, but its documentation is included in /bbmap/docs/guides/BBMapGuide.txt