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 131. 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
hg19.snp131Exceptions and hg19.snp131ExceptionDesc database tables):
- 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
(no instances of this exception were found in snp131)
- 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/snp131Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp131Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp131Mask/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp131Mask/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 2010-05-27 16:32 3.5K
chrY.subst.fa.gz 2010-05-27 14:29 8.0M
chrX.subst.fa.gz 2010-05-27 14:29 48M
chrUn_gl000248.subst.fa.gz 2010-05-27 14:29 13K
chrUn_gl000247.subst.fa.gz 2010-05-27 14:29 12K
chrUn_gl000246.subst.fa.gz 2010-05-27 14:29 13K
chrUn_gl000245.subst.fa.gz 2010-05-27 14:29 12K
chrUn_gl000244.subst.fa.gz 2010-05-27 14:29 13K
chrUn_gl000243.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000241.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000240.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000239.subst.fa.gz 2010-05-27 14:29 10K
chrUn_gl000238.subst.fa.gz 2010-05-27 14:29 13K
chrUn_gl000237.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000236.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000235.subst.fa.gz 2010-05-27 14:29 12K
chrUn_gl000234.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000233.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000232.subst.fa.gz 2010-05-27 14:29 14K
chrUn_gl000231.subst.fa.gz 2010-05-27 14:29 9.4K
chrUn_gl000230.subst.fa.gz 2010-05-27 14:29 13K
chrUn_gl000229.subst.fa.gz 2010-05-27 14:29 6.7K
chrUn_gl000228.subst.fa.gz 2010-05-27 14:29 33K
chrUn_gl000227.subst.fa.gz 2010-05-27 14:29 41K
chrUn_gl000226.subst.fa.gz 2010-05-27 14:29 3.5K
chrUn_gl000225.subst.fa.gz 2010-05-27 14:29 58K
chrUn_gl000224.subst.fa.gz 2010-05-27 14:29 51K
chrUn_gl000223.subst.fa.gz 2010-05-27 14:29 57K
chrUn_gl000222.subst.fa.gz 2010-05-27 14:29 60K
chrUn_gl000221.subst.fa.gz 2010-05-27 14:29 51K
chrUn_gl000220.subst.fa.gz 2010-05-27 14:29 54K
chrUn_gl000219.subst.fa.gz 2010-05-27 14:29 59K
chrUn_gl000218.subst.fa.gz 2010-05-27 14:29 55K
chrUn_gl000217.subst.fa.gz 2010-05-27 14:29 56K
chrUn_gl000216.subst.fa.gz 2010-05-27 14:29 43K
chrUn_gl000215.subst.fa.gz 2010-05-27 14:29 56K
chrUn_gl000214.subst.fa.gz 2010-05-27 14:29 44K
chrUn_gl000213.subst.fa.gz 2010-05-27 14:29 53K
chrUn_gl000212.subst.fa.gz 2010-05-27 14:29 62K
chrUn_gl000211.subst.fa.gz 2010-05-27 14:29 56K
chrM.subst.fa.gz 2010-05-27 14:29 6.0K
chr22.subst.fa.gz 2010-05-27 14:27 11M
chr21.subst.fa.gz 2010-05-27 14:27 11M
chr20.subst.fa.gz 2010-05-27 14:27 19M
chr19.subst.fa.gz 2010-05-27 14:27 17M
chr18.subst.fa.gz 2010-05-27 14:27 24M
chr17.subst.fa.gz 2010-05-27 14:26 25M
chr16.subst.fa.gz 2010-05-27 14:26 25M
chr15.subst.fa.gz 2010-05-27 14:26 26M
chr14.subst.fa.gz 2010-05-27 14:26 28M
chr13.subst.fa.gz 2010-05-27 14:26 31M
chr12.subst.fa.gz 2010-05-27 14:26 42M
chr11.subst.fa.gz 2010-05-27 14:25 42M
chr10.subst.fa.gz 2010-05-27 14:25 42M
chr9.subst.fa.gz 2010-05-27 14:29 39M
chr8.subst.fa.gz 2010-05-27 14:29 46M
chr7.subst.fa.gz 2010-05-27 14:29 50M
chr6.subst.fa.gz 2010-05-27 14:29 54M
chr5.subst.fa.gz 2010-05-27 14:28 57M
chr4.subst.fa.gz 2010-05-27 14:28 61M
chr3.subst.fa.gz 2010-05-27 14:28 63M
chr2.subst.fa.gz 2010-05-27 14:27 77M
chr1.subst.fa.gz 2010-05-27 14:25 72M