Hi all,
I'm mapping my reads (obtained from the MiSeq) to a reference genome using the Geneious software. It is a small bacterial genome.
Can anyone explain the following stats ?
Identical Sites: 1,801,496 (40.6%) Identical to reference genome ??
Pairwise % Identity: 99.0% Pairwise between what and what ?
Coverage of 4,439,218 bases:
Mean: 222.6 Std Dev: 63.5
Minimum: 0 Maximum: 533
Forward: ? Reverse: ?
Ref-Seq: 99.9% (4,408,919 of 4,411,532)
Does that mean that 99.9% of the reference genome has been covered ?
What does "ungapped length" mean?
The help function in the geneious software is not detailed.. I would appreciate any help !
Thanks !
I'm mapping my reads (obtained from the MiSeq) to a reference genome using the Geneious software. It is a small bacterial genome.
Can anyone explain the following stats ?
Identical Sites: 1,801,496 (40.6%) Identical to reference genome ??
Pairwise % Identity: 99.0% Pairwise between what and what ?
Coverage of 4,439,218 bases:
Mean: 222.6 Std Dev: 63.5
Minimum: 0 Maximum: 533
Forward: ? Reverse: ?
Ref-Seq: 99.9% (4,408,919 of 4,411,532)
Does that mean that 99.9% of the reference genome has been covered ?
What does "ungapped length" mean?
The help function in the geneious software is not detailed.. I would appreciate any help !
Thanks !
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