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
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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
[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
Name Last modified Size Description
Parent Directory -
md5sum.txt 2015-11-21 11:59 3.1K
chrUn_GL456390.subst.fa.gz 2015-11-21 10:37 3.5K
chr4_JH584292_random.subst.fa.gz 2015-11-21 10:37 4.9K
chrUn_GL456387.subst.fa.gz 2015-11-21 10:37 5.3K
chrUn_GL456381.subst.fa.gz 2015-11-21 10:37 5.3K
chrM.subst.fa.gz 2015-11-21 10:37 5.4K
chrUn_GL456370.subst.fa.gz 2015-11-21 10:37 6.0K
chrUn_GL456396.subst.fa.gz 2015-11-21 10:37 6.1K
chrUn_GL456392.subst.fa.gz 2015-11-21 10:37 6.6K
chrUn_GL456389.subst.fa.gz 2015-11-21 10:37 6.6K
chrUn_GL456394.subst.fa.gz 2015-11-21 10:37 7.0K
chrUn_GL456383.subst.fa.gz 2015-11-21 10:37 7.4K
chrUn_GL456382.subst.fa.gz 2015-11-21 10:37 7.7K
chrUn_GL456372.subst.fa.gz 2015-11-21 10:37 8.0K
chrUn_GL456359.subst.fa.gz 2015-11-21 10:37 8.1K
chrUn_GL456378.subst.fa.gz 2015-11-21 10:37 11K
chrUn_GL456360.subst.fa.gz 2015-11-21 10:37 11K
chrUn_GL456385.subst.fa.gz 2015-11-21 10:37 12K
chrUn_GL456239.subst.fa.gz 2015-11-21 10:37 13K
chrUn_GL456367.subst.fa.gz 2015-11-21 10:37 13K
chrUn_GL456393.subst.fa.gz 2015-11-21 10:37 13K
chrUn_GL456366.subst.fa.gz 2015-11-21 10:37 14K
chr4_GL456216_random.subst.fa.gz 2015-11-21 10:37 20K
chrUn_GL456379.subst.fa.gz 2015-11-21 10:37 23K
chrUn_JH584304.subst.fa.gz 2015-11-21 10:37 28K
chr1_GL456212_random.subst.fa.gz 2015-11-21 10:36 50K
chr1_GL456210_random.subst.fa.gz 2015-11-21 10:36 56K
chr4_JH584294_random.subst.fa.gz 2015-11-21 10:37 62K
chr4_JH584293_random.subst.fa.gz 2015-11-21 10:37 67K
chr1_GL456221_random.subst.fa.gz 2015-11-21 10:36 67K
chr1_GL456211_random.subst.fa.gz 2015-11-21 10:36 78K
chrY_JH584301_random.subst.fa.gz 2015-11-21 10:37 82K
chrX_GL456233_random.subst.fa.gz 2015-11-21 10:37 101K
chr5_JH584299_random.subst.fa.gz 2015-11-21 10:37 302K
chr19.subst.fa.gz 2015-11-21 10:36 20M
chrY.subst.fa.gz 2015-11-21 10:37 27M
chr18.subst.fa.gz 2015-11-21 10:36 30M
chr17.subst.fa.gz 2015-11-21 10:36 31M
chr16.subst.fa.gz 2015-11-21 10:36 33M
chr15.subst.fa.gz 2015-11-21 10:36 35M
chr12.subst.fa.gz 2015-11-21 10:36 40M
chr13.subst.fa.gz 2015-11-21 10:36 40M
chr11.subst.fa.gz 2015-11-21 10:36 41M
chr14.subst.fa.gz 2015-11-21 10:36 42M
chr9.subst.fa.gz 2015-11-21 10:37 42M
chr8.subst.fa.gz 2015-11-21 10:37 43M
chr10.subst.fa.gz 2015-11-21 10:35 44M
chr7.subst.fa.gz 2015-11-21 10:37 48M
chr6.subst.fa.gz 2015-11-21 10:37 50M
chr5.subst.fa.gz 2015-11-21 10:37 51M
chr4.subst.fa.gz 2015-11-21 10:37 52M
chr3.subst.fa.gz 2015-11-21 10:37 54M
chrX.subst.fa.gz 2015-11-21 10:37 54M
chr2.subst.fa.gz 2015-11-21 10:36 61M
chr1.subst.fa.gz 2015-11-21 10:35 66M