Ok, here is what BBMap stdout:
Code:
------------------ Results ------------------ Genome: 1 Key Length: 13 Max Indel: 16000 Minimum Score Ratio: 0.56 Mapping Mode: normal Reads Used: 72832 (9176832 bases) Mapping: 2.021 seconds. Reads/sec: 36044.03 kBases/sec: 4541.55 Pairing data: pct reads num reads pct bases num bases mated pairs: 0.1016% 37 0.1016% 9324 bad pairs: 0.0000% 0 0.0000% 0 insert size avg: 219.24 Read 1 data: pct reads num reads pct bases num bases mapped: 0.1181% 43 0.1181% 5418 unambiguous: 0.1181% 43 0.1181% 5418 ambiguous: 0.0000% 0 0.0000% 0 low-Q discards: 0.0137% 5 0.0137% 630 perfect best site: 0.0000% 0 0.0000% 0 semiperfect site: 0.0000% 0 0.0000% 0 rescued: 0.0220% 8 Match Rate: NA NA 84.0716% 4555 Error Rate: 100.0000% 43 15.8915% 861 Sub Rate: 100.0000% 43 15.2270% 825 Del Rate: 0.0000% 0 0.0000% 0 Ins Rate: 16.2791% 7 0.6645% 36 N Rate: 4.6512% 2 0.0369% 2 Read 2 data: pct reads num reads pct bases num bases mapped: 0.1428% 52 0.1428% 6552 unambiguous: 0.1428% 52 0.1428% 6552 ambiguous: 0.0000% 0 0.0000% 0 low-Q discards: 1.6751% 610 1.6751% 76860 perfect best site: 0.0000% 0 0.0000% 0 semiperfect site: 0.0000% 0 0.0000% 0 rescued: 0.0275% 10 Match Rate: NA NA 84.1270% 5512 Error Rate: 100.0000% 52 15.8730% 1040 Sub Rate: 100.0000% 52 15.8730% 1040 Del Rate: 0.0000% 0 0.0000% 0 Ins Rate: 0.0000% 0 0.0000% 0 N Rate: 0.0000% 0 0.0000% 0
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