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

Question

[kenneth.jh.han]

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

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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

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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?

Answer 1

[GenoMax]

See information about genome build "patches" here: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/patches.shtml

Mouse genome overview: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/

Answer 2

[sunhanice]

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.