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 147. 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.snp147 database table as well as the
hg19.snp147ExceptionDesc 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/snp147Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp147Mask/chr1.subst.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp147Mask/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp147Mask/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 2016-07-01 15:37 1.5K
chrUn_gl000226.subst.fa.gz 2016-07-01 15:39 2.6K
md5sum.txt 2016-07-01 15:42 5.3K
chrM.subst.fa.gz 2016-07-01 15:40 6.4K
chrUn_gl000229.subst.fa.gz 2016-07-01 15:39 6.7K
chr21_gl000210_random.subst.fa.gz 2016-07-01 15:38 9.0K
chrUn_gl000231.subst.fa.gz 2016-07-01 15:39 9.4K
chrUn_gl000239.subst.fa.gz 2016-07-01 15:39 11K
chrUn_gl000247.subst.fa.gz 2016-07-01 15:40 12K
chrUn_gl000235.subst.fa.gz 2016-07-01 15:39 12K
chr9_gl000201_random.subst.fa.gz 2016-07-01 15:39 12K
chrUn_gl000245.subst.fa.gz 2016-07-01 15:39 12K
chr8_gl000197_random.subst.fa.gz 2016-07-01 15:39 12K
chrUn_gl000246.subst.fa.gz 2016-07-01 15:39 13K
chr8_gl000196_random.subst.fa.gz 2016-07-01 15:39 13K
chrUn_gl000244.subst.fa.gz 2016-07-01 15:39 13K
chr17_gl000203_random.subst.fa.gz 2016-07-01 15:37 13K
chr17_gl000206_random.subst.fa.gz 2016-07-01 15:37 13K
chr11_gl000202_random.subst.fa.gz 2016-07-01 15:36 13K
chrUn_gl000238.subst.fa.gz 2016-07-01 15:39 13K
chrUn_gl000248.subst.fa.gz 2016-07-01 15:40 13K
chrUn_gl000230.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000240.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000236.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000243.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000232.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000234.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000233.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000241.subst.fa.gz 2016-07-01 15:39 14K
chrUn_gl000237.subst.fa.gz 2016-07-01 15:39 14K
chr9_gl000198_random.subst.fa.gz 2016-07-01 15:39 20K
chr19_gl000208_random.subst.fa.gz 2016-07-01 15:37 24K
chr17_gl000204_random.subst.fa.gz 2016-07-01 15:37 27K
chr9_gl000199_random.subst.fa.gz 2016-07-01 15:39 29K
chrUn_gl000228.subst.fa.gz 2016-07-01 15:39 33K
chr1_gl000191_random.subst.fa.gz 2016-07-01 15:37 33K
chrUn_gl000227.subst.fa.gz 2016-07-01 15:39 41K
chrUn_gl000216.subst.fa.gz 2016-07-01 15:39 43K
chrUn_gl000214.subst.fa.gz 2016-07-01 15:39 44K
chr19_gl000209_random.subst.fa.gz 2016-07-01 15:37 48K
chrUn_gl000224.subst.fa.gz 2016-07-01 15:39 51K
chrUn_gl000221.subst.fa.gz 2016-07-01 15:39 52K
chrUn_gl000213.subst.fa.gz 2016-07-01 15:39 53K
chrUn_gl000220.subst.fa.gz 2016-07-01 15:39 54K
chrUn_gl000218.subst.fa.gz 2016-07-01 15:39 56K
chrUn_gl000211.subst.fa.gz 2016-07-01 15:39 56K
chrUn_gl000217.subst.fa.gz 2016-07-01 15:39 56K
chrUn_gl000215.subst.fa.gz 2016-07-01 15:39 56K
chrUn_gl000223.subst.fa.gz 2016-07-01 15:39 57K
chr17_gl000205_random.subst.fa.gz 2016-07-01 15:37 57K
chrUn_gl000225.subst.fa.gz 2016-07-01 15:39 58K
chrUn_gl000219.subst.fa.gz 2016-07-01 15:39 59K
chrUn_gl000222.subst.fa.gz 2016-07-01 15:39 60K
chr9_gl000200_random.subst.fa.gz 2016-07-01 15:39 61K
chr4_gl000193_random.subst.fa.gz 2016-07-01 15:38 61K
chrUn_gl000212.subst.fa.gz 2016-07-01 15:39 62K
chr4_gl000194_random.subst.fa.gz 2016-07-01 15:39 66K
chr7_gl000195_random.subst.fa.gz 2016-07-01 15:39 66K
chr1_gl000192_random.subst.fa.gz 2016-07-01 15:37 178K
chr4_ctg9_hap1.subst.fa.gz 2016-07-01 15:38 221K
chr17_ctg5_hap1.subst.fa.gz 2016-07-01 15:37 554K
chr6_apd_hap1.subst.fa.gz 2016-07-01 15:39 893K
chr6_mcf_hap5.subst.fa.gz 2016-07-01 15:39 1.4M
chr6_mann_hap4.subst.fa.gz 2016-07-01 15:39 1.5M
chr6_ssto_hap7.subst.fa.gz 2016-07-01 15:39 1.5M
chr6_dbb_hap3.subst.fa.gz 2016-07-01 15:39 1.5M
chr6_qbl_hap6.subst.fa.gz 2016-07-01 15:39 1.6M
chr6_cox_hap2.subst.fa.gz 2016-07-01 15:39 1.7M
chrY.subst.fa.gz 2016-07-01 15:40 8.3M
chr22.subst.fa.gz 2016-07-01 15:38 13M
chr21.subst.fa.gz 2016-07-01 15:38 13M
chr19.subst.fa.gz 2016-07-01 15:37 20M
chr20.subst.fa.gz 2016-07-01 15:38 22M
chr18.subst.fa.gz 2016-07-01 15:37 27M
chr17.subst.fa.gz 2016-07-01 15:37 28M
chr16.subst.fa.gz 2016-07-01 15:37 29M
chr15.subst.fa.gz 2016-07-01 15:37 29M
chr14.subst.fa.gz 2016-07-01 15:37 32M
chr13.subst.fa.gz 2016-07-01 15:36 34M
chr9.subst.fa.gz 2016-07-01 15:39 43M
chr12.subst.fa.gz 2016-07-01 15:36 47M
chr10.subst.fa.gz 2016-07-01 15:36 47M
chr11.subst.fa.gz 2016-07-01 15:36 47M
chr8.subst.fa.gz 2016-07-01 15:39 52M
chrX.subst.fa.gz 2016-07-01 15:40 53M
chr7.subst.fa.gz 2016-07-01 15:39 56M
chr6.subst.fa.gz 2016-07-01 15:39 60M
chr5.subst.fa.gz 2016-07-01 15:39 64M
chr4.subst.fa.gz 2016-07-01 15:38 68M
chr3.subst.fa.gz 2016-07-01 15:38 70M
chr1.subst.fa.gz 2016-07-01 15:36 81M
chr2.subst.fa.gz 2016-07-01 15:37 86M