BBMap Scaffstats Understanding of Output

Question

[Ada]

Hello,

I would like to understand the meaning behind BBMap output scaffstats:

%unambiguousReads
unambiguousMB
%ambiguousReads ambiguousMB unambiguousReads
ambiguousReads
assignedReads
assignedBases

Answer 1

[GenoMax]

Unambiguous = Mapping to one reference sequence
Ambiguous = Mapping to more than one reference sequence
Read and Bases are just that.

[Ada]

Thank you for letting me know

[Ada]

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?