Discrepancy In The Number Of Scaffolds Of A Genome Assembly

Question

[nobrainw]

Hello,

I'm trying to figure out what to do with this genome assembly :

On this page http://www.ncbi.nlm.nih.gov/assembly/GCF_000002325.2/ the number of scaffolds mentionned in the stats is 6,173. In assembly definition just below I can only find 5,914 (5 + 5,909). I counted all scaffolds in the assembly report file and found it's actually 6,173.

My idea is this number includes the unlocalized scaffolds on each "chromosome". I'm wondering what is the most accurate genome representation. Should I include the unlocalized scaffolds (if that's what they are) and trust the assembly report file ? Or ignore them and stick with the 5,914 ?

Thanks !

Answer 1

[Neilfws]

Scroll down to the last table on that web page and click the tab named "Assembly Statistics".

You will see that chromosomes 1-5 have 85, 48, 44, 59 and 28 scaffolds mapped to them, respectively; the remaining 5 909 are unplaced.

Total = 6 173. So no discrepancy, just need to take care reading the information.

[nobrainw]

Thanks, I should have looked closer. Still wondering, are those scaffolds redundant with the chromosome sequences ? I mean, are they the scaffolds from which the chromosome sequences were built up ? Or some extra scaffolds of which exact position on each chromosome is unknown ?