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 - chr1.fa.gz 10-Sep-2020 15:39 60M chr10.fa.gz 10-Sep-2020 15:39 40M chr11.fa.gz 10-Sep-2020 15:39 37M chr12.fa.gz 10-Sep-2020 15:39 37M chr13.fa.gz 10-Sep-2020 15:39 37M chr14.fa.gz 10-Sep-2020 15:39 38M chr15.fa.gz 10-Sep-2020 15:39 32M chr16.fa.gz 10-Sep-2020 15:39 30M chr1_GL456210v1_random.fa.gz 10-Sep-2020 15:39 55K chr1_GL456211v1_random.fa.gz 10-Sep-2020 15:39 78K chr1_GL456212v1_random.fa.gz 10-Sep-2020 15:39 50K chr1_GL456221v1_random.fa.gz 10-Sep-2020 15:39 67K chr1_MU069434v1_random.fa.gz 10-Sep-2020 15:39 2.9K chr17.fa.gz 10-Sep-2020 15:39 29M chr18.fa.gz 10-Sep-2020 15:39 27M chr19.fa.gz 10-Sep-2020 15:39 18M chr1_GL456239v1_random.fa.gz 10-Sep-2020 15:39 12K chr2.fa.gz 10-Sep-2020 15:39 56M chr3.fa.gz 10-Sep-2020 15:39 49M chr4.fa.gz 10-Sep-2020 15:39 48M chr4_JH584295v1_random.fa.gz 10-Sep-2020 15:39 757 chr5.fa.gz 10-Sep-2020 15:39 46M chr5_GL456354v1_random.fa.gz 10-Sep-2020 15:39 63K chr5_JH584296v1_random.fa.gz 10-Sep-2020 15:39 64K chr5_JH584297v1_random.fa.gz 10-Sep-2020 15:39 66K chr5_JH584298v1_random.fa.gz 10-Sep-2020 15:39 59K chr5_JH584299v1_random.fa.gz 10-Sep-2020 15:39 302K chr6.fa.gz 10-Sep-2020 15:39 46M chr7.fa.gz 10-Sep-2020 15:39 44M chr7_GL456219v1_random.fa.gz 10-Sep-2020 15:39 56K chr8.fa.gz 10-Sep-2020 15:39 39M chr9.fa.gz 10-Sep-2020 15:39 38M chrM.fa.gz 10-Sep-2020 15:39 5.3K chrUn_GL456359v1.fa.gz 10-Sep-2020 15:39 7.8K chrUn_GL456360v1.fa.gz 10-Sep-2020 15:39 11K chrUn_GL456366v1.fa.gz 10-Sep-2020 15:39 14K chrUn_GL456367v1.fa.gz 10-Sep-2020 15:39 13K chrUn_GL456368v1.fa.gz 10-Sep-2020 15:39 6.7K chrUn_GL456370v1.fa.gz 10-Sep-2020 15:39 5.7K chrUn_GL456372v1.fa.gz 10-Sep-2020 15:39 8.1K chrUn_GL456378v1.fa.gz 10-Sep-2020 15:39 10K chrUn_GL456379v1.fa.gz 10-Sep-2020 15:39 23K chrUn_GL456381v1.fa.gz 10-Sep-2020 15:39 5.1K chrUn_GL456382v1.fa.gz 10-Sep-2020 15:39 7.6K chrUn_GL456383v1.fa.gz 10-Sep-2020 15:39 7.1K chrUn_GL456385v1.fa.gz 10-Sep-2020 15:39 12K chrUn_GL456387v1.fa.gz 10-Sep-2020 15:39 4.9K chrUn_GL456389v1.fa.gz 10-Sep-2020 15:39 6.4K chrUn_GL456390v1.fa.gz 10-Sep-2020 15:39 3.3K chrUn_GL456392v1.fa.gz 10-Sep-2020 15:39 6.4K chrUn_GL456394v1.fa.gz 10-Sep-2020 15:39 6.8K chrUn_GL456396v1.fa.gz 10-Sep-2020 15:39 5.9K chrUn_JH584304v1.fa.gz 10-Sep-2020 15:39 28K chrUn_MU069435v1.fa.gz 10-Sep-2020 15:39 7.7K chrX.fa.gz 10-Sep-2020 15:39 51M chrX_GL456233v2_random.fa.gz 10-Sep-2020 15:39 154K chrY.fa.gz 10-Sep-2020 15:39 28M chrY_JH584300v1_random.fa.gz 10-Sep-2020 15:39 59K chrY_JH584301v1_random.fa.gz 10-Sep-2020 15:39 82K chrY_JH584302v1_random.fa.gz 10-Sep-2020 15:39 50K chrY_JH584303v1_random.fa.gz 10-Sep-2020 15:39 51K md5sum.txt 10-Sep-2020 15:50 3.3K