**10**wrote:

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`

Since you are looking at two

E.coligenomes 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.87k