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 135. 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.snp135 database table as well as the
hg19.snp135ExceptionDesc 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/snp135Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp135Mask/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 2011-11-14 14:47 1.8K
chrM.subst.fa.gz 2011-11-14 14:33 6.1K
chr4_ctg9_hap1.subst.fa.gz 2011-11-14 14:31 196K
chr17_ctg5_hap1.subst.fa.gz 2011-11-14 14:25 512K
chr6_apd_hap1.subst.fa.gz 2011-11-14 14:31 803K
chr6_mcf_hap5.subst.fa.gz 2011-11-14 14:31 1.3M
chr6_mann_hap4.subst.fa.gz 2011-11-14 14:31 1.3M
chr6_dbb_hap3.subst.fa.gz 2011-11-14 14:31 1.4M
chr6_ssto_hap7.subst.fa.gz 2011-11-14 14:32 1.4M
chr6_qbl_hap6.subst.fa.gz 2011-11-14 14:32 1.4M
chr6_cox_hap2.subst.fa.gz 2011-11-14 14:31 1.6M
chrY.subst.fa.gz 2011-11-14 14:33 8.0M
chr22.subst.fa.gz 2011-11-14 14:30 12M
chr21.subst.fa.gz 2011-11-14 14:29 12M
chr19.subst.fa.gz 2011-11-14 14:27 18M
chr20.subst.fa.gz 2011-11-14 14:28 20M
chr18.subst.fa.gz 2011-11-14 14:27 25M
chr17.subst.fa.gz 2011-11-14 14:25 26M
chr16.subst.fa.gz 2011-11-14 14:25 26M
chr15.subst.fa.gz 2011-11-14 14:25 27M
chr14.subst.fa.gz 2011-11-14 14:25 29M
chr13.subst.fa.gz 2011-11-14 14:24 32M
chr9.subst.fa.gz 2011-11-14 14:32 40M
chr12.subst.fa.gz 2011-11-14 14:24 43M
chr11.subst.fa.gz 2011-11-14 14:23 44M
chr10.subst.fa.gz 2011-11-14 14:23 44M
chr8.subst.fa.gz 2011-11-14 14:32 48M
chrX.subst.fa.gz 2011-11-14 14:33 49M
chr7.subst.fa.gz 2011-11-14 14:32 51M
chr6.subst.fa.gz 2011-11-14 14:31 56M
chr5.subst.fa.gz 2011-11-14 14:31 59M
chr4.subst.fa.gz 2011-11-14 14:31 63M
chr3.subst.fa.gz 2011-11-14 14:30 65M
chr1.subst.fa.gz 2011-11-14 14:22 75M
chr2.subst.fa.gz 2011-11-14 14:27 79M