This directory contains FASTA files which contain a modified version
of the Genome Reference Consortium mouse genome build 38 (mm10, Dec. 2011). 
The chromosomal sequences were assembled by the Mouse Genome Reference
Consortium.  The mm10/GRCm38 assembly was changed to use IUPAC ambiguous 
nucleotide characters at each base covered by a stringently filtered subset 
of single-base substitutions annotated by dbSNP build 142.  For example, 
if the assembly has an 'A' at a position where dbSNP has annotated an A/C/T 
substitution SNP, the 'A' is replaced by 'H' in the FASTA file here.  

dbSNP single-base substitutions were excluded from masking in the
following cases:
- UCSC tagged the dbSNP item with any of these exceptions (see also the
  exceptions field of the mm10.snp142 database table as well as the
  mm10.snp142ExceptionDesc table):
  - MultipleAlignments: dbSNP mapped item to multiple locations
  - ObservedMismatch: the reference allele does not appear in the item's
    observed alleles.
  - ObservedWrongFormat: the observed sequence has an unexpected format
- dbSNP item class is not "single".
- dbSNP item length is not exactly one base.
- dbSNP item weight is greater than 1.  (lower weight = higher confidence)
The remaining single-base substitutions were used to mask the genomic 
sequence.

Files included in this directory:

chr*.subst.fa.gz - FASTA files with IUPAC characters for substitution SNPs

md5sum.txt - checksums of files in this directory

------------------------------------------------------------------
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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/mm10/snp142Mask. 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/snp142Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/snp142Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/snp142Mask/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/snp142Mask/chr1.subst.fa.gz' \
        -O chr1.subst.fa.gz

To uncompress the fa.gz files:
    gunzip <file>.fa.gz

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt23-Nov-2015 09:51 2.6K 
[   ]chr1.subst.fa.gz21-Nov-2015 10:35 66M 
[   ]chr1_GL456210_random.subst.fa.gz21-Nov-2015 10:36 56K 
[   ]chr1_GL456211_random.subst.fa.gz21-Nov-2015 10:36 78K 
[   ]chr1_GL456212_random.subst.fa.gz21-Nov-2015 10:36 50K 
[   ]chr1_GL456221_random.subst.fa.gz21-Nov-2015 10:36 67K 
[   ]chr2.subst.fa.gz21-Nov-2015 10:36 61M 
[   ]chr3.subst.fa.gz21-Nov-2015 10:37 54M 
[   ]chr4.subst.fa.gz21-Nov-2015 10:37 52M 
[   ]chr4_GL456216_random.subst.fa.gz21-Nov-2015 10:37 20K 
[   ]chr4_JH584292_random.subst.fa.gz21-Nov-2015 10:37 4.9K 
[   ]chr4_JH584293_random.subst.fa.gz21-Nov-2015 10:37 67K 
[   ]chr4_JH584294_random.subst.fa.gz21-Nov-2015 10:37 62K 
[   ]chr5.subst.fa.gz21-Nov-2015 10:37 51M 
[   ]chr5_JH584299_random.subst.fa.gz21-Nov-2015 10:37 302K 
[   ]chr6.subst.fa.gz21-Nov-2015 10:37 50M 
[   ]chr7.subst.fa.gz21-Nov-2015 10:37 48M 
[   ]chr8.subst.fa.gz21-Nov-2015 10:37 43M 
[   ]chr9.subst.fa.gz21-Nov-2015 10:37 42M 
[   ]chr10.subst.fa.gz21-Nov-2015 10:35 44M 
[   ]chr11.subst.fa.gz21-Nov-2015 10:36 41M 
[   ]chr12.subst.fa.gz21-Nov-2015 10:36 40M 
[   ]chr13.subst.fa.gz21-Nov-2015 10:36 40M 
[   ]chr14.subst.fa.gz21-Nov-2015 10:36 42M 
[   ]chr15.subst.fa.gz21-Nov-2015 10:36 35M 
[   ]chr16.subst.fa.gz21-Nov-2015 10:36 33M 
[   ]chr17.subst.fa.gz21-Nov-2015 10:36 31M 
[   ]chr18.subst.fa.gz21-Nov-2015 10:36 30M 
[   ]chr19.subst.fa.gz21-Nov-2015 10:36 20M 
[   ]chrM.subst.fa.gz21-Nov-2015 10:37 5.4K 
[   ]chrUn_GL456239.subst.fa.gz21-Nov-2015 10:37 13K 
[   ]chrUn_GL456359.subst.fa.gz21-Nov-2015 10:37 8.1K 
[   ]chrUn_GL456360.subst.fa.gz21-Nov-2015 10:37 11K 
[   ]chrUn_GL456366.subst.fa.gz21-Nov-2015 10:37 14K 
[   ]chrUn_GL456367.subst.fa.gz21-Nov-2015 10:37 13K 
[   ]chrUn_GL456370.subst.fa.gz21-Nov-2015 10:37 6.0K 
[   ]chrUn_GL456372.subst.fa.gz21-Nov-2015 10:37 8.0K 
[   ]chrUn_GL456378.subst.fa.gz21-Nov-2015 10:37 11K 
[   ]chrUn_GL456379.subst.fa.gz21-Nov-2015 10:37 23K 
[   ]chrUn_GL456381.subst.fa.gz21-Nov-2015 10:37 5.3K 
[   ]chrUn_GL456382.subst.fa.gz21-Nov-2015 10:37 7.7K 
[   ]chrUn_GL456383.subst.fa.gz21-Nov-2015 10:37 7.4K 
[   ]chrUn_GL456385.subst.fa.gz21-Nov-2015 10:37 12K 
[   ]chrUn_GL456387.subst.fa.gz21-Nov-2015 10:37 5.3K 
[   ]chrUn_GL456389.subst.fa.gz21-Nov-2015 10:37 6.6K 
[   ]chrUn_GL456390.subst.fa.gz21-Nov-2015 10:37 3.5K 
[   ]chrUn_GL456392.subst.fa.gz21-Nov-2015 10:37 6.6K 
[   ]chrUn_GL456393.subst.fa.gz21-Nov-2015 10:37 13K 
[   ]chrUn_GL456394.subst.fa.gz21-Nov-2015 10:37 7.0K 
[   ]chrUn_GL456396.subst.fa.gz21-Nov-2015 10:37 6.1K 
[   ]chrUn_JH584304.subst.fa.gz21-Nov-2015 10:37 28K 
[   ]chrX.subst.fa.gz21-Nov-2015 10:37 54M 
[   ]chrX_GL456233_random.subst.fa.gz21-Nov-2015 10:37 101K 
[   ]chrY.subst.fa.gz21-Nov-2015 10:37 27M 
[   ]chrY_JH584301_random.subst.fa.gz21-Nov-2015 10:37 82K 
[TXT]md5sum.txt21-Nov-2015 11:59 3.1K 

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