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 - md5sum.txt 2012-02-09 14:17 3.5K chrY_JH584303_random.fa.gz 2012-02-09 13:40 51K chrY_JH584302_random.fa.gz 2012-02-09 13:40 50K chrY_JH584301_random.fa.gz 2012-02-09 13:40 82K chrY_JH584300_random.fa.gz 2012-02-09 13:40 59K chrY.fa.gz 2012-02-09 13:40 27M chrX_GL456233_random.fa.gz 2012-02-09 13:40 100K chrX.fa.gz 2012-02-09 13:38 51M chrUn_JH584304.fa.gz 2012-02-09 13:40 28K chrUn_GL456396.fa.gz 2012-02-09 13:40 6.0K chrUn_GL456394.fa.gz 2012-02-09 13:40 6.9K chrUn_GL456393.fa.gz 2012-02-09 13:40 13K chrUn_GL456392.fa.gz 2012-02-09 13:40 6.4K chrUn_GL456390.fa.gz 2012-02-09 13:40 3.3K chrUn_GL456389.fa.gz 2012-02-09 13:40 6.5K chrUn_GL456387.fa.gz 2012-02-09 13:40 5.1K chrUn_GL456385.fa.gz 2012-02-09 13:40 12K chrUn_GL456383.fa.gz 2012-02-09 13:40 7.2K chrUn_GL456382.fa.gz 2012-02-09 13:40 7.6K chrUn_GL456381.fa.gz 2012-02-09 13:40 5.2K chrUn_GL456379.fa.gz 2012-02-09 13:40 23K chrUn_GL456378.fa.gz 2012-02-09 13:40 10K chrUn_GL456372.fa.gz 2012-02-09 13:40 8.0K chrUn_GL456370.fa.gz 2012-02-09 13:40 5.8K chrUn_GL456368.fa.gz 2012-02-09 13:40 6.7K chrUn_GL456367.fa.gz 2012-02-09 13:40 13K chrUn_GL456366.fa.gz 2012-02-09 13:40 14K chrUn_GL456360.fa.gz 2012-02-09 13:40 11K chrUn_GL456359.fa.gz 2012-02-09 13:40 7.8K chrUn_GL456239.fa.gz 2012-02-09 13:40 12K chrM.fa.gz 2012-02-09 13:40 5.3K chr19.fa.gz 2012-02-09 13:40 18M chr18.fa.gz 2012-02-09 13:40 27M chr17.fa.gz 2012-02-09 13:40 29M chr16.fa.gz 2012-02-09 13:40 30M chr15.fa.gz 2012-02-09 13:40 32M chr14.fa.gz 2012-02-09 13:39 38M chr13.fa.gz 2012-02-09 13:39 37M chr12.fa.gz 2012-02-09 13:40 37M chr11.fa.gz 2012-02-09 13:39 37M chr10.fa.gz 2012-02-09 13:39 40M chr9.fa.gz 2012-02-09 13:39 38M chr8.fa.gz 2012-02-09 13:39 39M chr7_GL456219_random.fa.gz 2012-02-09 13:40 56K chr7.fa.gz 2012-02-09 13:39 44M chr6.fa.gz 2012-02-09 13:39 46M chr5_JH584299_random.fa.gz 2012-02-09 13:40 302K chr5_JH584298_random.fa.gz 2012-02-09 13:40 59K chr5_JH584297_random.fa.gz 2012-02-09 13:40 66K chr5_JH584296_random.fa.gz 2012-02-09 13:40 64K chr5_GL456354_random.fa.gz 2012-02-09 13:40 63K chr5.fa.gz 2012-02-09 13:39 46M chr4_JH584295_random.fa.gz 2012-02-09 13:40 757 chr4_JH584294_random.fa.gz 2012-02-09 13:40 62K chr4_JH584293_random.fa.gz 2012-02-09 13:40 67K chr4_JH584292_random.fa.gz 2012-02-09 13:40 4.9K chr4_GL456350_random.fa.gz 2012-02-09 13:40 72K chr4_GL456216_random.fa.gz 2012-02-09 13:40 20K chr4.fa.gz 2012-02-09 13:39 48M chr3.fa.gz 2012-02-09 13:39 49M chr2.fa.gz 2012-02-09 13:38 56M chr1_GL456221_random.fa.gz 2012-02-09 13:40 67K chr1_GL456213_random.fa.gz 2012-02-09 13:40 13K chr1_GL456212_random.fa.gz 2012-02-09 13:40 50K chr1_GL456211_random.fa.gz 2012-02-09 13:40 78K chr1_GL456210_random.fa.gz 2012-02-09 13:40 55K chr1.fa.gz 2012-02-09 13:38 60M