BBMap Scaffstats Understanding of Output
1 answer
For instance:
name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases
NZ_GG773477.1 Escherichia coli MS 116-1 Scfld976, whole genome shotgun sequence 4.93292 31.023300 0.00021 0.001350 206822 9 208715 31307250
This means that 4.9% of the input read aligned to the shotgun sequence? On the same token 0.001350 % is ambiguous, matching to more than one reference sequence. For the latter, how does bbmap determine that the read has mapped to more than one reference sequence?
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