Hello, I would like assistance understanding the following results below:
What is the fraction that "%unambiguousReads" is out of? Essentially, how do they come up with the fraction. What determines the denominator? In addition, if the fraction is 0.87 does this mean 87%? or 0.87%?
What is the fraction that "%ambiguousReads" is out of? Essentially, how do they come up with the fraction. What determines the denominator?
What does assignedReads mean?
What does assignedBases mean?
What does the MB mean in unambiguousMB/ambiguousMB?
name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases NC_009801.1 Escherichia coli O139:H28 str. E24377A, complete sequence 0.87367 7.1124 4.07912 33.2073 47416 221382 111291 16693650 NZ_GG773290.1 Escherichia coli MS 78-1 Scfld327, whole genome shotgun sequence 0.34082 2.77455 0.05644 0.45945 18497 3063 18747 2812050
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Ada •
2 answers
I don't know what BBMap does specifically, but typically the denominator is the total number of reads, or the total number of mapped reads, depending on the circumstance.
In this case, it seems that the total number of reads was not reported in the statistics, hence we can't check that assumption.
I would expect that assigned means reads that the read could be mapped (assigned to a location).
I would expect that unambiguous means that a read maps to a single location.
I would expect that ambiguous means that a read maps equally well to more than one location.
The MB means megabase (millions of bases)
Total number of reads is reported in BBMap/BBsplit stats. OP has not included that information. Typical result looks like this:
Genome: 1
Key Length: 13
Max Indel: 20
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 53236 (7985400 bases)
Mapping: 46.016 seconds.
Reads/sec: 1156.89
kBases/sec: 173.53
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 86.2236% 22951 86.2236% 6885300
bad pairs: 2.1527% 573 2.1527% 171900
insert size avg: 435.68
Read 1 data: pct reads num reads pct bases num bases
mapped: 91.7499% 24422 91.7499% 3663300
unambiguous: 87.2943% 23236 87.2943% 3485400
ambiguous: 4.4556% 1186 4.4556% 177900
low-Q discards: 0.0000% 0 0.0000% 0
In fact output posted by original poster is for bbsplit.sh refstats option. So these result needs to be taken into consideration with the main output of bbsplit.sh run which looks like the bbmap.sh I posted above (bbsplit.sh uses bbmap.sh under the covers to do the read binning). Example of that looks like:
#name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases
human 88.33496 7.053900 0.30806 0.024600 47026 164 47026 7053900
mouse 6.07108 0.484800 0.30806 0.024600 3232 164 3396 509400
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BBMap Scaffstats Understanding of Output
written by Ada •
Since you are looking at two E.coli genomes it is not surprising that the % unambiguous reads is very small. No aligner is going to be able to distinguish between very similar genomes of the same species especially when short reads are being used. I am curious as to where the remaining 95% of reads are since they do not seem to be accounted for by these two lines.