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

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
• 3,095 views • link
updated by Ram Ram • written by kenneth.jh.han • kenneth.jh.han

2 answers

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/

• 0 views • link
written by GenoMax GenoMax

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.

• 0 views • link
updated by Ram Ram • written by sunhanice sunhanice

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