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 144.  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.snp144 database table as well as the
  hg19.snp144ExceptionDesc 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/snp144Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp144Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp144Mask/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp144Mask/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 2015-09-09 13:23 81M chr1_gl000191_random.subst.fa.gz 2015-09-09 13:24 33K chr1_gl000192_random.subst.fa.gz 2015-09-09 13:24 178K chr2.subst.fa.gz 2015-09-09 13:24 86M chr3.subst.fa.gz 2015-09-09 13:25 70M chr4.subst.fa.gz 2015-09-09 13:25 67M chr4_ctg9_hap1.subst.fa.gz 2015-09-09 13:25 193K chr4_gl000193_random.subst.fa.gz 2015-09-09 13:25 61K chr4_gl000194_random.subst.fa.gz 2015-09-09 13:26 65K chr5.subst.fa.gz 2015-09-09 13:26 64M chr6.subst.fa.gz 2015-09-09 13:26 60M chr6_apd_hap1.subst.fa.gz 2015-09-09 13:26 784K chr6_cox_hap2.subst.fa.gz 2015-09-09 13:26 1.5M chr6_dbb_hap3.subst.fa.gz 2015-09-09 13:26 1.3M chr6_mann_hap4.subst.fa.gz 2015-09-09 13:26 1.3M chr6_mcf_hap5.subst.fa.gz 2015-09-09 13:26 1.2M chr6_qbl_hap6.subst.fa.gz 2015-09-09 13:26 1.4M chr6_ssto_hap7.subst.fa.gz 2015-09-09 13:26 1.3M chr7.subst.fa.gz 2015-09-09 13:26 55M chr7_gl000195_random.subst.fa.gz 2015-09-09 13:26 66K chr8.subst.fa.gz 2015-09-09 13:26 52M chr8_gl000196_random.subst.fa.gz 2015-09-09 13:26 13K chr8_gl000197_random.subst.fa.gz 2015-09-09 13:26 12K chr9.subst.fa.gz 2015-09-09 13:26 43M chr9_gl000198_random.subst.fa.gz 2015-09-09 13:26 20K chr9_gl000199_random.subst.fa.gz 2015-09-09 13:26 28K chr9_gl000200_random.subst.fa.gz 2015-09-09 13:26 61K chr9_gl000201_random.subst.fa.gz 2015-09-09 13:26 12K chr10.subst.fa.gz 2015-09-09 13:23 47M chr11.subst.fa.gz 2015-09-09 13:23 47M chr11_gl000202_random.subst.fa.gz 2015-09-09 13:23 13K chr12.subst.fa.gz 2015-09-09 13:23 47M chr13.subst.fa.gz 2015-09-09 13:23 34M chr14.subst.fa.gz 2015-09-09 13:24 32M chr15.subst.fa.gz 2015-09-09 13:24 29M chr16.subst.fa.gz 2015-09-09 13:24 29M chr17.subst.fa.gz 2015-09-09 13:24 28M chr17_ctg5_hap1.subst.fa.gz 2015-09-09 13:24 520K chr17_gl000203_random.subst.fa.gz 2015-09-09 13:24 13K chr17_gl000204_random.subst.fa.gz 2015-09-09 13:24 27K chr17_gl000205_random.subst.fa.gz 2015-09-09 13:24 57K chr17_gl000206_random.subst.fa.gz 2015-09-09 13:24 13K chr18.subst.fa.gz 2015-09-09 13:24 27M chr18_gl000207_random.subst.fa.gz 2015-09-09 13:24 1.5K chr19.subst.fa.gz 2015-09-09 13:24 20M chr19_gl000208_random.subst.fa.gz 2015-09-09 13:24 24K chr19_gl000209_random.subst.fa.gz 2015-09-09 13:24 48K chr20.subst.fa.gz 2015-09-09 13:25 21M chr21.subst.fa.gz 2015-09-09 13:25 13M chr21_gl000210_random.subst.fa.gz 2015-09-09 13:25 9.0K chr22.subst.fa.gz 2015-09-09 13:25 13M chrM.subst.fa.gz 2015-09-09 13:27 6.5K chrUn_gl000211.subst.fa.gz 2015-09-09 13:26 56K chrUn_gl000212.subst.fa.gz 2015-09-09 13:26 62K chrUn_gl000213.subst.fa.gz 2015-09-09 13:26 53K chrUn_gl000214.subst.fa.gz 2015-09-09 13:26 43K chrUn_gl000215.subst.fa.gz 2015-09-09 13:26 56K chrUn_gl000216.subst.fa.gz 2015-09-09 13:26 43K chrUn_gl000217.subst.fa.gz 2015-09-09 13:26 56K chrUn_gl000218.subst.fa.gz 2015-09-09 13:26 56K chrUn_gl000219.subst.fa.gz 2015-09-09 13:26 59K chrUn_gl000220.subst.fa.gz 2015-09-09 13:26 54K chrUn_gl000221.subst.fa.gz 2015-09-09 13:26 52K chrUn_gl000222.subst.fa.gz 2015-09-09 13:26 60K chrUn_gl000223.subst.fa.gz 2015-09-09 13:26 57K chrUn_gl000224.subst.fa.gz 2015-09-09 13:26 51K chrUn_gl000225.subst.fa.gz 2015-09-09 13:26 58K chrUn_gl000226.subst.fa.gz 2015-09-09 13:26 2.6K chrUn_gl000227.subst.fa.gz 2015-09-09 13:26 41K chrUn_gl000228.subst.fa.gz 2015-09-09 13:26 33K chrUn_gl000229.subst.fa.gz 2015-09-09 13:26 6.7K chrUn_gl000230.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000231.subst.fa.gz 2015-09-09 13:26 9.4K chrUn_gl000232.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000233.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000234.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000235.subst.fa.gz 2015-09-09 13:26 12K chrUn_gl000236.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000237.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000238.subst.fa.gz 2015-09-09 13:26 13K chrUn_gl000239.subst.fa.gz 2015-09-09 13:26 11K chrUn_gl000240.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000241.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000243.subst.fa.gz 2015-09-09 13:26 14K chrUn_gl000244.subst.fa.gz 2015-09-09 13:26 13K chrUn_gl000245.subst.fa.gz 2015-09-09 13:26 12K chrUn_gl000246.subst.fa.gz 2015-09-09 13:26 13K chrUn_gl000247.subst.fa.gz 2015-09-09 13:27 12K chrUn_gl000248.subst.fa.gz 2015-09-09 13:27 13K chrX.subst.fa.gz 2015-09-09 13:27 51M chrY.subst.fa.gz 2015-09-09 13:27 8.3M md5sum.txt 2015-09-09 13:43 5.3K