This directory contains FASTA files which contain a modified version
of the Feb. 2009 (GRCh37/hg19) reference human genome assembly.
The chromosomal sequences were assembled by the International Human
Genome Project sequencing centers. The assembly sequence 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 151. 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.snp151 database table as well as the
hg19.snp151ExceptionDesc 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.soe.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.soe.ucsc.edu/goldenPath/hg19/snp151Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/snp151Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/snp151Mask/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/snp151Mask/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 -
chr18_gl000207_random.subst.fa.gz 2018-04-17 13:09 2.0K
chrUn_gl000226.subst.fa.gz 2018-04-17 13:17 2.6K
md5sum.txt 2018-04-17 13:20 5.4K
chr21_gl000210_random.subst.fa.gz 2018-04-17 13:12 9.1K
chrUn_gl000229.subst.fa.gz 2018-04-17 13:17 11K
chrUn_gl000247.subst.fa.gz 2018-04-17 13:17 12K
chr9_gl000201_random.subst.fa.gz 2018-04-17 13:17 12K
chr8_gl000197_random.subst.fa.gz 2018-04-17 13:17 12K
chrUn_gl000246.subst.fa.gz 2018-04-17 13:17 13K
chrUn_gl000249.subst.fa.gz 2018-04-17 13:18 13K
chr17_gl000206_random.subst.fa.gz 2018-04-17 13:09 13K
chrUn_gl000238.subst.fa.gz 2018-04-17 13:17 13K
chrUn_gl000248.subst.fa.gz 2018-04-17 13:18 13K
chrUn_gl000239.subst.fa.gz 2018-04-17 13:17 14K
chr17_gl000203_random.subst.fa.gz 2018-04-17 13:08 14K
chrUn_gl000242.subst.fa.gz 2018-04-17 13:17 14K
chrUn_gl000245.subst.fa.gz 2018-04-17 13:17 15K
chrUn_gl000231.subst.fa.gz 2018-04-17 13:17 15K
chrUn_gl000236.subst.fa.gz 2018-04-17 13:17 16K
chrUn_gl000244.subst.fa.gz 2018-04-17 13:17 16K
chr11_gl000202_random.subst.fa.gz 2018-04-17 13:06 16K
chrUn_gl000237.subst.fa.gz 2018-04-17 13:17 16K
chr8_gl000196_random.subst.fa.gz 2018-04-17 13:17 17K
chrUn_gl000230.subst.fa.gz 2018-04-17 13:17 17K
chrUn_gl000235.subst.fa.gz 2018-04-17 13:17 19K
chrUn_gl000232.subst.fa.gz 2018-04-17 13:17 20K
chrUn_gl000233.subst.fa.gz 2018-04-17 13:17 21K
chrUn_gl000234.subst.fa.gz 2018-04-17 13:17 22K
chrUn_gl000240.subst.fa.gz 2018-04-17 13:17 22K
chrUn_gl000241.subst.fa.gz 2018-04-17 13:17 22K
chrUn_gl000243.subst.fa.gz 2018-04-17 13:17 22K
chr19_gl000208_random.subst.fa.gz 2018-04-17 13:09 24K
chr9_gl000198_random.subst.fa.gz 2018-04-17 13:17 26K
chr17_gl000204_random.subst.fa.gz 2018-04-17 13:08 33K
chrUn_gl000228.subst.fa.gz 2018-04-17 13:17 33K
chr1_gl000191_random.subst.fa.gz 2018-04-17 13:10 34K
chrUn_gl000227.subst.fa.gz 2018-04-17 13:17 41K
chrUn_gl000216.subst.fa.gz 2018-04-17 13:17 43K
chrUn_gl000214.subst.fa.gz 2018-04-17 13:17 44K
chr19_gl000209_random.subst.fa.gz 2018-04-17 13:09 48K
chrUn_gl000224.subst.fa.gz 2018-04-17 13:17 52K
chrUn_gl000221.subst.fa.gz 2018-04-17 13:17 52K
chrUn_gl000213.subst.fa.gz 2018-04-17 13:17 54K
chrUn_gl000220.subst.fa.gz 2018-04-17 13:17 54K
chrUn_gl000215.subst.fa.gz 2018-04-17 13:17 56K
chrUn_gl000223.subst.fa.gz 2018-04-17 13:17 57K
chrUn_gl000218.subst.fa.gz 2018-04-17 13:17 58K
chrUn_gl000225.subst.fa.gz 2018-04-17 13:17 58K
chr17_gl000205_random.subst.fa.gz 2018-04-17 13:09 58K
chrUn_gl000219.subst.fa.gz 2018-04-17 13:17 59K
chr9_gl000200_random.subst.fa.gz 2018-04-17 13:17 61K
chrUn_gl000212.subst.fa.gz 2018-04-17 13:17 63K
chrUn_gl000222.subst.fa.gz 2018-04-17 13:17 64K
chr7_gl000195_random.subst.fa.gz 2018-04-17 13:17 67K
chr4_gl000194_random.subst.fa.gz 2018-04-17 13:15 67K
chr9_gl000199_random.subst.fa.gz 2018-04-17 13:17 70K
chrUn_gl000217.subst.fa.gz 2018-04-17 13:17 78K
chrUn_gl000211.subst.fa.gz 2018-04-17 13:17 82K
chr4_gl000193_random.subst.fa.gz 2018-04-17 13:14 91K
chr4_ctg9_hap1.subst.fa.gz 2018-04-17 13:13 234K
chr1_gl000192_random.subst.fa.gz 2018-04-17 13:10 235K
chr17_ctg5_hap1.subst.fa.gz 2018-04-17 13:08 571K
chr6_apd_hap1.subst.fa.gz 2018-04-17 13:15 930K
chr6_mcf_hap5.subst.fa.gz 2018-04-17 13:15 1.5M
chr6_mann_hap4.subst.fa.gz 2018-04-17 13:15 1.6M
chr6_ssto_hap7.subst.fa.gz 2018-04-17 13:16 1.6M
chr6_dbb_hap3.subst.fa.gz 2018-04-17 13:15 1.6M
chr6_qbl_hap6.subst.fa.gz 2018-04-17 13:16 1.6M
chr6_cox_hap2.subst.fa.gz 2018-04-17 13:15 1.8M
chrY.subst.fa.gz 2018-04-17 13:18 8.6M
chr22.subst.fa.gz 2018-04-17 13:13 15M
chr21.subst.fa.gz 2018-04-17 13:11 15M
chr19.subst.fa.gz 2018-04-17 13:09 24M
chr20.subst.fa.gz 2018-04-17 13:11 26M
chr18.subst.fa.gz 2018-04-17 13:09 33M
chr17.subst.fa.gz 2018-04-17 13:08 34M
chr16.subst.fa.gz 2018-04-17 13:08 35M
chr15.subst.fa.gz 2018-04-17 13:08 36M
chr14.subst.fa.gz 2018-04-17 13:08 39M
chr13.subst.fa.gz 2018-04-17 13:07 42M
chr9.subst.fa.gz 2018-04-17 13:17 53M
chr12.subst.fa.gz 2018-04-17 13:07 57M
chr10.subst.fa.gz 2018-04-17 13:06 57M
chr11.subst.fa.gz 2018-04-17 13:06 57M
chrX.subst.fa.gz 2018-04-17 13:18 61M
chr8.subst.fa.gz 2018-04-17 13:17 63M
chr7.subst.fa.gz 2018-04-17 13:17 68M
chr6.subst.fa.gz 2018-04-17 13:15 73M
chr5.subst.fa.gz 2018-04-17 13:15 78M
chr4.subst.fa.gz 2018-04-17 13:13 82M
chr3.subst.fa.gz 2018-04-17 13:13 85M
chr1.subst.fa.gz 2018-04-17 13:05 98M
chr2.subst.fa.gz 2018-04-17 13:11 104M