This directory contains the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome
(mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)) in one gzip-compressed FASTA file per chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
This assembly was produced by the Mouse Genome Sequencing Consortium,
and the National Center for Biotechnology Information (NCBI).
For more information on the mouse genome, see the project website:
See also: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
http://www.ncbi.nlm.nih.gov/genome/52
Files included in this directory:
- chr*.fa.gz: compressed FASTA sequence of each chromosome.
Each chromosome is in a separate file in a gzip Fasta format.
Repeats -- which are shown in lower case -- are annotated by
RepeatMasker run at the sensitive setting and Tandem Repeats Finder
(repeats of period 12 or less).
- md5sum.txt - MD5 checksum of these files to verify correct transmission
The main assembly is contained in the chrN.fa.gz files, where N is the name
of the chromosome. The chrN_random.fa.gz files contain clones that are not
yet finished or cannot be placed with certainty at a specific place on
the chromosome. The chrUn_random.fa.gz sequence are unfinished clones,
or clones that can not be tenatively placed on any chromosome.
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If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then
go to the directory goldenPath/mm10/chromosomes. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/chrM.fa.gz'
-O chrM.fa.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
All the files in this directory are freely available for public use.
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This file last updated: 2012-02-09 - 09 February 2012
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Name Last modified Size Description
Parent Directory -
chr1.fa.gz 09-Feb-2012 13:38 60M
chr1_GL456210_random.fa.gz 09-Feb-2012 13:40 55K
chr1_GL456211_random.fa.gz 09-Feb-2012 13:40 78K
chr1_GL456212_random.fa.gz 09-Feb-2012 13:40 50K
chr1_GL456213_random.fa.gz 09-Feb-2012 13:40 13K
chr1_GL456221_random.fa.gz 09-Feb-2012 13:40 67K
chr2.fa.gz 09-Feb-2012 13:38 56M
chr3.fa.gz 09-Feb-2012 13:39 49M
chr4.fa.gz 09-Feb-2012 13:39 48M
chr4_GL456216_random.fa.gz 09-Feb-2012 13:40 20K
chr4_GL456350_random.fa.gz 09-Feb-2012 13:40 72K
chr4_JH584292_random.fa.gz 09-Feb-2012 13:40 4.9K
chr4_JH584293_random.fa.gz 09-Feb-2012 13:40 67K
chr4_JH584294_random.fa.gz 09-Feb-2012 13:40 62K
chr4_JH584295_random.fa.gz 09-Feb-2012 13:40 757
chr5.fa.gz 09-Feb-2012 13:39 46M
chr5_GL456354_random.fa.gz 09-Feb-2012 13:40 63K
chr5_JH584296_random.fa.gz 09-Feb-2012 13:40 64K
chr5_JH584297_random.fa.gz 09-Feb-2012 13:40 66K
chr5_JH584298_random.fa.gz 09-Feb-2012 13:40 59K
chr5_JH584299_random.fa.gz 09-Feb-2012 13:40 302K
chr6.fa.gz 09-Feb-2012 13:39 46M
chr7.fa.gz 09-Feb-2012 13:39 44M
chr7_GL456219_random.fa.gz 09-Feb-2012 13:40 56K
chr8.fa.gz 09-Feb-2012 13:39 39M
chr9.fa.gz 09-Feb-2012 13:39 38M
chr10.fa.gz 09-Feb-2012 13:39 40M
chr11.fa.gz 09-Feb-2012 13:39 37M
chr12.fa.gz 09-Feb-2012 13:40 37M
chr13.fa.gz 09-Feb-2012 13:39 37M
chr14.fa.gz 09-Feb-2012 13:39 38M
chr15.fa.gz 09-Feb-2012 13:40 32M
chr16.fa.gz 09-Feb-2012 13:40 30M
chr17.fa.gz 09-Feb-2012 13:40 29M
chr18.fa.gz 09-Feb-2012 13:40 27M
chr19.fa.gz 09-Feb-2012 13:40 18M
chrM.fa.gz 09-Feb-2012 13:40 5.3K
chrUn_GL456239.fa.gz 09-Feb-2012 13:40 12K
chrUn_GL456359.fa.gz 09-Feb-2012 13:40 7.8K
chrUn_GL456360.fa.gz 09-Feb-2012 13:40 11K
chrUn_GL456366.fa.gz 09-Feb-2012 13:40 14K
chrUn_GL456367.fa.gz 09-Feb-2012 13:40 13K
chrUn_GL456368.fa.gz 09-Feb-2012 13:40 6.7K
chrUn_GL456370.fa.gz 09-Feb-2012 13:40 5.8K
chrUn_GL456372.fa.gz 09-Feb-2012 13:40 8.0K
chrUn_GL456378.fa.gz 09-Feb-2012 13:40 10K
chrUn_GL456379.fa.gz 09-Feb-2012 13:40 23K
chrUn_GL456381.fa.gz 09-Feb-2012 13:40 5.2K
chrUn_GL456382.fa.gz 09-Feb-2012 13:40 7.6K
chrUn_GL456383.fa.gz 09-Feb-2012 13:40 7.2K
chrUn_GL456385.fa.gz 09-Feb-2012 13:40 12K
chrUn_GL456387.fa.gz 09-Feb-2012 13:40 5.1K
chrUn_GL456389.fa.gz 09-Feb-2012 13:40 6.5K
chrUn_GL456390.fa.gz 09-Feb-2012 13:40 3.3K
chrUn_GL456392.fa.gz 09-Feb-2012 13:40 6.4K
chrUn_GL456393.fa.gz 09-Feb-2012 13:40 13K
chrUn_GL456394.fa.gz 09-Feb-2012 13:40 6.9K
chrUn_GL456396.fa.gz 09-Feb-2012 13:40 6.0K
chrUn_JH584304.fa.gz 09-Feb-2012 13:40 28K
chrX.fa.gz 09-Feb-2012 13:38 51M
chrX_GL456233_random.fa.gz 09-Feb-2012 13:40 100K
chrY.fa.gz 09-Feb-2012 13:40 27M
chrY_JH584300_random.fa.gz 09-Feb-2012 13:40 59K
chrY_JH584301_random.fa.gz 09-Feb-2012 13:40 82K
chrY_JH584302_random.fa.gz 09-Feb-2012 13:40 50K
chrY_JH584303_random.fa.gz 09-Feb-2012 13:40 51K
md5sum.txt 09-Feb-2012 14:17 3.5K