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 - chr1.subst.fa.gz 2018-04-17 13:05 98M chr1_gl000191_random.subst.fa.gz 2018-04-17 13:10 34K chr1_gl000192_random.subst.fa.gz 2018-04-17 13:10 235K chr2.subst.fa.gz 2018-04-17 13:11 104M chr3.subst.fa.gz 2018-04-17 13:13 85M chr4.subst.fa.gz 2018-04-17 13:13 82M chr4_ctg9_hap1.subst.fa.gz 2018-04-17 13:13 234K chr4_gl000193_random.subst.fa.gz 2018-04-17 13:14 91K chr4_gl000194_random.subst.fa.gz 2018-04-17 13:15 67K chr5.subst.fa.gz 2018-04-17 13:15 78M chr6.subst.fa.gz 2018-04-17 13:15 73M chr6_apd_hap1.subst.fa.gz 2018-04-17 13:15 930K chr6_cox_hap2.subst.fa.gz 2018-04-17 13:15 1.8M chr6_dbb_hap3.subst.fa.gz 2018-04-17 13:15 1.6M chr6_mann_hap4.subst.fa.gz 2018-04-17 13:15 1.6M chr6_mcf_hap5.subst.fa.gz 2018-04-17 13:15 1.5M chr6_qbl_hap6.subst.fa.gz 2018-04-17 13:16 1.6M chr6_ssto_hap7.subst.fa.gz 2018-04-17 13:16 1.6M chr7.subst.fa.gz 2018-04-17 13:17 68M chr7_gl000195_random.subst.fa.gz 2018-04-17 13:17 67K chr8.subst.fa.gz 2018-04-17 13:17 63M chr8_gl000196_random.subst.fa.gz 2018-04-17 13:17 17K chr8_gl000197_random.subst.fa.gz 2018-04-17 13:17 12K chr9.subst.fa.gz 2018-04-17 13:17 53M chr9_gl000198_random.subst.fa.gz 2018-04-17 13:17 26K chr9_gl000199_random.subst.fa.gz 2018-04-17 13:17 70K chr9_gl000200_random.subst.fa.gz 2018-04-17 13:17 61K chr9_gl000201_random.subst.fa.gz 2018-04-17 13:17 12K chr10.subst.fa.gz 2018-04-17 13:06 57M chr11.subst.fa.gz 2018-04-17 13:06 57M chr11_gl000202_random.subst.fa.gz 2018-04-17 13:06 16K chr12.subst.fa.gz 2018-04-17 13:07 57M chr13.subst.fa.gz 2018-04-17 13:07 42M chr14.subst.fa.gz 2018-04-17 13:08 39M chr15.subst.fa.gz 2018-04-17 13:08 36M chr16.subst.fa.gz 2018-04-17 13:08 35M chr17.subst.fa.gz 2018-04-17 13:08 34M chr17_ctg5_hap1.subst.fa.gz 2018-04-17 13:08 571K chr17_gl000203_random.subst.fa.gz 2018-04-17 13:08 14K chr17_gl000204_random.subst.fa.gz 2018-04-17 13:08 33K chr17_gl000205_random.subst.fa.gz 2018-04-17 13:09 58K chr17_gl000206_random.subst.fa.gz 2018-04-17 13:09 13K chr18.subst.fa.gz 2018-04-17 13:09 33M chr18_gl000207_random.subst.fa.gz 2018-04-17 13:09 2.0K chr19.subst.fa.gz 2018-04-17 13:09 24M chr19_gl000208_random.subst.fa.gz 2018-04-17 13:09 24K chr19_gl000209_random.subst.fa.gz 2018-04-17 13:09 48K chr20.subst.fa.gz 2018-04-17 13:11 26M chr21.subst.fa.gz 2018-04-17 13:11 15M chr21_gl000210_random.subst.fa.gz 2018-04-17 13:12 9.1K chr22.subst.fa.gz 2018-04-17 13:13 15M chrUn_gl000211.subst.fa.gz 2018-04-17 13:17 82K chrUn_gl000212.subst.fa.gz 2018-04-17 13:17 63K chrUn_gl000213.subst.fa.gz 2018-04-17 13:17 54K chrUn_gl000214.subst.fa.gz 2018-04-17 13:17 44K chrUn_gl000215.subst.fa.gz 2018-04-17 13:17 56K chrUn_gl000216.subst.fa.gz 2018-04-17 13:17 43K chrUn_gl000217.subst.fa.gz 2018-04-17 13:17 78K chrUn_gl000218.subst.fa.gz 2018-04-17 13:17 58K chrUn_gl000219.subst.fa.gz 2018-04-17 13:17 59K chrUn_gl000220.subst.fa.gz 2018-04-17 13:17 54K chrUn_gl000221.subst.fa.gz 2018-04-17 13:17 52K chrUn_gl000222.subst.fa.gz 2018-04-17 13:17 64K chrUn_gl000223.subst.fa.gz 2018-04-17 13:17 57K chrUn_gl000224.subst.fa.gz 2018-04-17 13:17 52K chrUn_gl000225.subst.fa.gz 2018-04-17 13:17 58K chrUn_gl000226.subst.fa.gz 2018-04-17 13:17 2.6K chrUn_gl000227.subst.fa.gz 2018-04-17 13:17 41K chrUn_gl000228.subst.fa.gz 2018-04-17 13:17 33K chrUn_gl000229.subst.fa.gz 2018-04-17 13:17 11K chrUn_gl000230.subst.fa.gz 2018-04-17 13:17 17K chrUn_gl000231.subst.fa.gz 2018-04-17 13:17 15K 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_gl000235.subst.fa.gz 2018-04-17 13:17 19K chrUn_gl000236.subst.fa.gz 2018-04-17 13:17 16K chrUn_gl000237.subst.fa.gz 2018-04-17 13:17 16K chrUn_gl000238.subst.fa.gz 2018-04-17 13:17 13K chrUn_gl000239.subst.fa.gz 2018-04-17 13:17 14K chrUn_gl000240.subst.fa.gz 2018-04-17 13:17 22K chrUn_gl000241.subst.fa.gz 2018-04-17 13:17 22K chrUn_gl000242.subst.fa.gz 2018-04-17 13:17 14K chrUn_gl000243.subst.fa.gz 2018-04-17 13:17 22K chrUn_gl000244.subst.fa.gz 2018-04-17 13:17 16K chrUn_gl000245.subst.fa.gz 2018-04-17 13:17 15K chrUn_gl000246.subst.fa.gz 2018-04-17 13:17 13K chrUn_gl000247.subst.fa.gz 2018-04-17 13:17 12K chrUn_gl000248.subst.fa.gz 2018-04-17 13:18 13K chrUn_gl000249.subst.fa.gz 2018-04-17 13:18 13K chrX.subst.fa.gz 2018-04-17 13:18 61M chrY.subst.fa.gz 2018-04-17 13:18 8.6M md5sum.txt 2018-04-17 13:20 5.4K