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
- 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
- MultipleAlignments: dbSNP mapped item to multiple locations
- ObservedMismatch: the reference allele does not appear in the item's
- 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
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 \
Or with wget, all files:
wget --timestamping \
With wget, a single file:
wget --timestamping \
To uncompress the fa.gz files:
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80