Between mm10.p4 and mm10, why the total sequence length different?
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7.1 years ago

Hi, My name is Kenneth.

I found that mm10.p4 and mm10 the total length of sequence is different in websites. (NCBI, Ensembl ..)

http://www.ebi.ac.uk/ena/data/view/GCA_000001635.6

http://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.24

http://www.ncbi.nlm.nih.gov/assembly/327618


mm10.p4:

Total length: 2,803,568,840

Ungapped length: 2,724,212,084

mm10:

Total length: 2,793,712,140

Ungapped length: 2,714,420,385


I downloaded the FASTA files and counted ACTGN bases, resulted in the number of Nucleotides are same between mm10.p4 and mm10.

But why the "Total length", "Ungapped length" are different between mm10.p4 and mm10?

Assembly Reference mm10 mouse-genome • 2.1k views
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7.1 years ago
sunhanice ▴ 240

From my understanding, total number of nucleotides may be different. But, the number of nucleotides on the major chromosomes (chr1, chr2, ..., chrX, chrY) should be kept the same for the same version reference.

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