This directory contains FASTA files which contain a modified version
of the Genome Reference Consortium human genome build 37 (hg19, Feb. 2009).
The chromosomal sequences were assembled by the International Human
Genome Project sequencing centers. The hg19/GRCh37 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 141. 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 hg19.snp141 database table as well as the
hg19.snp141ExceptionDesc 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/hg19/bigZips. 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/hg19/snp141Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp141Mask/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 2014-08-29 17:02 1.3K
chrY.subst.fa.gz 2014-08-29 16:26 8.1M
chrX.subst.fa.gz 2014-08-29 16:26 50M
chrM.subst.fa.gz 2014-08-29 16:26 6.4K
chr22.subst.fa.gz 2014-08-29 16:25 12M
chr21.subst.fa.gz 2014-08-29 16:25 12M
chr20.subst.fa.gz 2014-08-29 16:25 20M
chr19.subst.fa.gz 2014-08-29 16:25 18M
chr18.subst.fa.gz 2014-08-29 16:25 25M
chr17.subst.fa.gz 2014-08-29 16:25 26M
chr16.subst.fa.gz 2014-08-29 16:24 27M
chr15.subst.fa.gz 2014-08-29 16:24 27M
chr14.subst.fa.gz 2014-08-29 16:24 30M
chr13.subst.fa.gz 2014-08-29 16:24 32M
chr12.subst.fa.gz 2014-08-29 16:24 44M
chr11.subst.fa.gz 2014-08-29 16:24 44M
chr10.subst.fa.gz 2014-08-29 16:24 44M
chr9.subst.fa.gz 2014-08-29 16:26 40M
chr8.subst.fa.gz 2014-08-29 16:26 48M
chr7.subst.fa.gz 2014-08-29 16:26 52M
chr6.subst.fa.gz 2014-08-29 16:26 56M
chr5.subst.fa.gz 2014-08-29 16:25 60M
chr4.subst.fa.gz 2014-08-29 16:25 63M
chr3.subst.fa.gz 2014-08-29 16:25 66M
chr2.subst.fa.gz 2014-08-29 16:25 80M
chr1.subst.fa.gz 2014-08-29 16:24 75M