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 138. 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.snp138 database table as well as the
hg19.snp138ExceptionDesc 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/snp138Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp138Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp138Mask/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp138Mask/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 -
chr7.fa 2013-08-01 12:08 155M
chrX.fa 2013-08-01 12:09 151M
chr8.fa 2013-08-01 12:08 142M
chr9.fa 2013-08-01 12:08 137M
chr2.subst.fa.gz 2014-03-31 14:03 80M
chr1.subst.fa.gz 2014-03-31 14:02 76M
chr3.subst.fa.gz 2014-03-31 14:03 66M
chr4.subst.fa.gz 2014-03-31 14:03 63M
chr5.subst.fa.gz 2014-03-31 14:03 60M
chrY.fa 2013-08-01 12:09 58M
chr6.subst.fa.gz 2014-03-31 14:03 56M
chr7.subst.fa.gz 2014-03-31 14:03 52M
chrX.subst.fa.gz 2014-03-31 14:04 50M
chr8.subst.fa.gz 2014-03-31 14:04 48M
chr11.subst.fa.gz 2014-03-31 14:02 44M
chr10.subst.fa.gz 2014-03-31 14:02 44M
chr12.subst.fa.gz 2014-03-31 14:02 44M
chr9.subst.fa.gz 2014-03-31 14:04 40M
chr13.subst.fa.gz 2014-03-31 14:02 32M
chr14.subst.fa.gz 2014-03-31 14:02 30M
chr15.subst.fa.gz 2014-03-31 14:02 27M
chr16.subst.fa.gz 2014-03-31 14:02 27M
chr17.subst.fa.gz 2014-03-31 14:02 26M
chr18.subst.fa.gz 2014-03-31 14:02 25M
chr20.subst.fa.gz 2014-03-31 14:03 20M
chr19.subst.fa.gz 2014-03-31 14:02 18M
chr21.subst.fa.gz 2014-03-31 14:03 12M
chr22.subst.fa.gz 2014-03-31 14:03 12M
chrY.subst.fa.gz 2014-03-31 14:04 8.1M
chr6_ssto_hap7.fa 2013-08-01 12:08 4.8M
chr6_mcf_hap5.fa 2013-08-01 12:07 4.7M
chr6_mann_hap4.fa 2013-08-01 12:07 4.6M
chr6_qbl_hap6.fa 2013-08-01 12:08 4.5M
chr6_cox_hap2.subst.fa.gz 2014-03-31 14:03 1.6M
chr6_qbl_hap6.subst.fa.gz 2014-03-31 14:03 1.4M
chr6_ssto_hap7.subst.fa.gz 2014-03-31 14:03 1.4M
chr6_dbb_hap3.subst.fa.gz 2014-03-31 14:03 1.4M
chr6_mann_hap4.subst.fa.gz 2014-03-31 14:03 1.4M
chr6_mcf_hap5.subst.fa.gz 2014-03-31 14:03 1.3M
chr6_apd_hap1.subst.fa.gz 2014-03-31 14:03 819K
chr17_ctg5_hap1.subst.fa.gz 2014-03-31 14:02 516K
chrUn_gl000225.fa 2013-08-01 12:08 210K
chr4_ctg9_hap1.subst.fa.gz 2014-03-31 14:03 199K
chr9_gl000200_random.fa 2013-08-01 12:08 186K
chrUn_gl000222.fa 2013-08-01 12:08 186K
chrUn_gl000212.fa 2013-08-01 12:08 186K
chr7_gl000195_random.fa 2013-08-01 12:08 182K
chrUn_gl000223.fa 2013-08-01 12:08 180K
chrUn_gl000224.fa 2013-08-01 12:08 179K
chrUn_gl000219.fa 2013-08-01 12:08 179K
chr1_gl000192_random.subst.fa.gz 2014-03-31 14:03 178K
chrUn_gl000215.fa 2013-08-01 12:08 172K
chrUn_gl000216.fa 2013-08-01 12:08 172K
chrUn_gl000217.fa 2013-08-01 12:08 171K
chr9_gl000199_random.fa 2013-08-01 12:08 169K
chrUn_gl000211.fa 2013-08-01 12:08 166K
chrUn_gl000213.fa 2013-08-01 12:08 164K
chrUn_gl000220.fa 2013-08-01 12:08 161K
chrUn_gl000218.fa 2013-08-01 12:08 161K
chrUn_gl000221.fa 2013-08-01 12:08 155K
chrUn_gl000214.fa 2013-08-01 12:08 137K
chrUn_gl000228.fa 2013-08-01 12:08 129K
chrUn_gl000227.fa 2013-08-01 12:08 128K
chr9_gl000198_random.fa 2013-08-01 12:08 90K
chr7_gl000195_random.subst.fa.gz 2014-03-31 14:03 65K
chr4_gl000194_random.subst.fa.gz 2014-03-31 14:03 65K
chrUn_gl000212.subst.fa.gz 2014-03-31 14:04 62K
chr4_gl000193_random.subst.fa.gz 2014-03-31 14:03 61K
chr9_gl000200_random.subst.fa.gz 2014-03-31 14:04 61K
chrUn_gl000222.subst.fa.gz 2014-03-31 14:04 60K
chrUn_gl000219.subst.fa.gz 2014-03-31 14:04 59K
chr17_gl000205_random.subst.fa.gz 2014-03-31 14:02 58K
chrUn_gl000225.subst.fa.gz 2014-03-31 14:04 58K
chrUn_gl000223.subst.fa.gz 2014-03-31 14:04 57K
chrUn_gl000215.subst.fa.gz 2014-03-31 14:04 56K
chrUn_gl000217.subst.fa.gz 2014-03-31 14:04 56K
chrUn_gl000211.subst.fa.gz 2014-03-31 14:04 56K
chrUn_gl000218.subst.fa.gz 2014-03-31 14:04 55K
chrUn_gl000220.subst.fa.gz 2014-03-31 14:04 54K
chrUn_gl000213.subst.fa.gz 2014-03-31 14:04 53K
chrUn_gl000221.subst.fa.gz 2014-03-31 14:04 51K
chrUn_gl000224.subst.fa.gz 2014-03-31 14:04 51K
chr19_gl000209_random.subst.fa.gz 2014-03-31 14:02 47K
chrUn_gl000233.fa 2013-08-01 12:08 46K
chrUn_gl000237.fa 2013-08-01 12:08 46K
chrUn_gl000214.subst.fa.gz 2014-03-31 14:04 44K
chrUn_gl000230.fa 2013-08-01 12:08 44K
chrUn_gl000243.fa 2013-08-01 12:08 43K
chrUn_gl000216.subst.fa.gz 2014-03-31 14:04 43K
chrUn_gl000241.fa 2013-08-01 12:08 42K
chrUn_gl000236.fa 2013-08-01 12:08 42K
chrUn_gl000240.fa 2013-08-01 12:08 42K
chrUn_gl000227.subst.fa.gz 2014-03-31 14:04 41K
chrUn_gl000232.fa 2013-08-01 12:08 41K
chrUn_gl000234.fa 2013-08-01 12:08 40K
chrUn_gl000238.fa 2013-08-01 12:08 40K
chrUn_gl000244.fa 2013-08-01 12:08 40K
chrUn_gl000248.fa 2013-08-01 12:09 40K
chrUn_gl000246.fa 2013-08-01 12:08 38K
chr8_gl000197_random.fa 2013-08-01 12:08 37K
chrUn_gl000245.fa 2013-08-01 12:08 37K
chrUn_gl000247.fa 2013-08-01 12:09 36K
chr9_gl000201_random.fa 2013-08-01 12:08 36K
chrUn_gl000235.fa 2013-08-01 12:08 34K
chrUn_gl000239.fa 2013-08-01 12:08 34K
chr1_gl000191_random.subst.fa.gz 2014-03-31 14:03 33K
chrUn_gl000228.subst.fa.gz 2014-03-31 14:04 33K
chr9_gl000199_random.subst.fa.gz 2014-03-31 14:04 31K
chrUn_gl000231.fa 2013-08-01 12:08 27K
chr17_gl000204_random.subst.fa.gz 2014-03-31 14:02 26K
chr19_gl000208_random.subst.fa.gz 2014-03-31 14:02 24K
chr9_gl000198_random.subst.fa.gz 2014-03-31 14:04 20K
chrUn_gl000229.fa 2013-08-01 12:08 20K
chrM.fa 2013-08-01 12:09 17K
chrUn_gl000226.fa 2013-08-01 12:08 15K
chrUn_gl000237.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000241.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000233.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000234.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000232.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000236.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000243.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000240.subst.fa.gz 2014-03-31 14:04 14K
chrUn_gl000248.subst.fa.gz 2014-03-31 14:04 13K
chrUn_gl000238.subst.fa.gz 2014-03-31 14:04 13K
chrUn_gl000230.subst.fa.gz 2014-03-31 14:04 13K
chr11_gl000202_random.subst.fa.gz 2014-03-31 14:02 13K
chr17_gl000206_random.subst.fa.gz 2014-03-31 14:02 13K
chr17_gl000203_random.subst.fa.gz 2014-03-31 14:02 13K
chrUn_gl000244.subst.fa.gz 2014-03-31 14:04 13K
chrUn_gl000246.subst.fa.gz 2014-03-31 14:04 13K
chr8_gl000197_random.subst.fa.gz 2014-03-31 14:04 12K
chrUn_gl000245.subst.fa.gz 2014-03-31 14:04 12K
chr9_gl000201_random.subst.fa.gz 2014-03-31 14:04 12K
chrUn_gl000235.subst.fa.gz 2014-03-31 14:04 12K
chrUn_gl000247.subst.fa.gz 2014-03-31 14:04 11K
chrUn_gl000239.subst.fa.gz 2014-03-31 14:04 10K
chrUn_gl000231.subst.fa.gz 2014-03-31 14:04 9.4K
chr21_gl000210_random.subst.fa.gz 2014-03-31 14:03 9.0K
chrUn_gl000229.subst.fa.gz 2014-03-31 14:04 6.7K
chrM.subst.fa.gz 2014-03-31 14:04 6.4K
md5sum.txt 2014-03-31 15:08 5.2K
chrUn_gl000226.subst.fa.gz 2014-03-31 14:04 2.9K
chr18_gl000207_random.subst.fa.gz 2014-03-31 14:02 1.5K