This directory contains the June 2020 (GRCm39/mm39) assembly of the mouse genome
(mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)),
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/
https://www.ncbi.nlm.nih.gov/genome/52
https://www.ncbi.nlm.nih.gov/genome/assembly/7358741
https://www.ncbi.nlm.nih.gov/bioproject/20689
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/mm39/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/mm39/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/mm39/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm39/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm39/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: 2020-09-10 - 10 September 2020
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Name Last modified Size Description
Parent Directory -
md5sum.txt 2020-09-10 15:50 3.3K
chrY_JH584303v1_random.fa.gz 2020-09-10 15:39 51K
chrY_JH584302v1_random.fa.gz 2020-09-10 15:39 50K
chrY_JH584301v1_random.fa.gz 2020-09-10 15:39 82K
chrY_JH584300v1_random.fa.gz 2020-09-10 15:39 59K
chrY.fa.gz 2020-09-10 15:39 28M
chrX_GL456233v2_random.fa.gz 2020-09-10 15:39 154K
chrX.fa.gz 2020-09-10 15:39 51M
chrUn_MU069435v1.fa.gz 2020-09-10 15:39 7.7K
chrUn_JH584304v1.fa.gz 2020-09-10 15:39 28K
chrUn_GL456396v1.fa.gz 2020-09-10 15:39 5.9K
chrUn_GL456394v1.fa.gz 2020-09-10 15:39 6.8K
chrUn_GL456392v1.fa.gz 2020-09-10 15:39 6.4K
chrUn_GL456390v1.fa.gz 2020-09-10 15:39 3.3K
chrUn_GL456389v1.fa.gz 2020-09-10 15:39 6.4K
chrUn_GL456387v1.fa.gz 2020-09-10 15:39 4.9K
chrUn_GL456385v1.fa.gz 2020-09-10 15:39 12K
chrUn_GL456383v1.fa.gz 2020-09-10 15:39 7.1K
chrUn_GL456382v1.fa.gz 2020-09-10 15:39 7.6K
chrUn_GL456381v1.fa.gz 2020-09-10 15:39 5.1K
chrUn_GL456379v1.fa.gz 2020-09-10 15:39 23K
chrUn_GL456378v1.fa.gz 2020-09-10 15:39 10K
chrUn_GL456372v1.fa.gz 2020-09-10 15:39 8.1K
chrUn_GL456370v1.fa.gz 2020-09-10 15:39 5.7K
chrUn_GL456368v1.fa.gz 2020-09-10 15:39 6.7K
chrUn_GL456367v1.fa.gz 2020-09-10 15:39 13K
chrUn_GL456366v1.fa.gz 2020-09-10 15:39 14K
chrUn_GL456360v1.fa.gz 2020-09-10 15:39 11K
chrUn_GL456359v1.fa.gz 2020-09-10 15:39 7.8K
chrM.fa.gz 2020-09-10 15:39 5.3K
chr19.fa.gz 2020-09-10 15:39 18M
chr18.fa.gz 2020-09-10 15:39 27M
chr17.fa.gz 2020-09-10 15:39 29M
chr16.fa.gz 2020-09-10 15:39 30M
chr15.fa.gz 2020-09-10 15:39 32M
chr14.fa.gz 2020-09-10 15:39 38M
chr13.fa.gz 2020-09-10 15:39 37M
chr12.fa.gz 2020-09-10 15:39 37M
chr11.fa.gz 2020-09-10 15:39 37M
chr10.fa.gz 2020-09-10 15:39 40M
chr9.fa.gz 2020-09-10 15:39 38M
chr8.fa.gz 2020-09-10 15:39 39M
chr7_GL456219v1_random.fa.gz 2020-09-10 15:39 56K
chr7.fa.gz 2020-09-10 15:39 44M
chr6.fa.gz 2020-09-10 15:39 46M
chr5_JH584299v1_random.fa.gz 2020-09-10 15:39 302K
chr5_JH584298v1_random.fa.gz 2020-09-10 15:39 59K
chr5_JH584297v1_random.fa.gz 2020-09-10 15:39 66K
chr5_JH584296v1_random.fa.gz 2020-09-10 15:39 64K
chr5_GL456354v1_random.fa.gz 2020-09-10 15:39 63K
chr5.fa.gz 2020-09-10 15:39 46M
chr4_JH584295v1_random.fa.gz 2020-09-10 15:39 757
chr4.fa.gz 2020-09-10 15:39 48M
chr3.fa.gz 2020-09-10 15:39 49M
chr2.fa.gz 2020-09-10 15:39 56M
chr1_MU069434v1_random.fa.gz 2020-09-10 15:39 2.9K
chr1_GL456239v1_random.fa.gz 2020-09-10 15:39 12K
chr1_GL456221v1_random.fa.gz 2020-09-10 15:39 67K
chr1_GL456212v1_random.fa.gz 2020-09-10 15:39 50K
chr1_GL456211v1_random.fa.gz 2020-09-10 15:39 78K
chr1_GL456210v1_random.fa.gz 2020-09-10 15:39 55K
chr1.fa.gz 2020-09-10 15:39 60M