Understanding BBMAP output
BBMap short read aligner, and other bioinformatic tools.
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#39 Understanding BBMAP output
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
Assistance is needed to understand BBMAP outputs. I have ~20K of these and would like to be able to understand what I am processing.
Essentially, what is %unambiguousReads and %ambiguousReads out of? How do those numbers come about? Are they the overall alignment score for that particular contig?
For ambiguousreads where do they match to?
What is unambiguousMB vs ambiguousMB?
What is assignedreads and assignedbases?