Question: Between mm10.p4 and mm10, why the total sequence length different?
0
gravatar for kenneth.jh.han
3.4 years ago by
Korea, Republic Of
kenneth.jh.han0 wrote:

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?

 

ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 3.4 years ago by kenneth.jh.han0
0
gravatar for genomax
3.4 years ago by
genomax63k
United States
genomax63k wrote:

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/

ADD COMMENTlink written 3.4 years ago by genomax63k
0
gravatar for sunhanice
3.4 years ago by
sunhanice190
United States
sunhanice190 wrote:

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.

ADD COMMENTlink written 3.4 years ago by sunhanice190
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