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

------------------------------------------------------------------
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

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt09-Sep-2015 13:43 2.6K 
[   ]chr1.subst.fa.gz09-Sep-2015 13:23 81M 
[   ]chr1_gl000191_random.subst.fa.gz09-Sep-2015 13:24 33K 
[   ]chr1_gl000192_random.subst.fa.gz09-Sep-2015 13:24 178K 
[   ]chr2.subst.fa.gz09-Sep-2015 13:24 86M 
[   ]chr3.subst.fa.gz09-Sep-2015 13:25 70M 
[   ]chr4.subst.fa.gz09-Sep-2015 13:25 67M 
[   ]chr4_ctg9_hap1.subst.fa.gz09-Sep-2015 13:25 193K 
[   ]chr4_gl000193_random.subst.fa.gz09-Sep-2015 13:25 61K 
[   ]chr4_gl000194_random.subst.fa.gz09-Sep-2015 13:26 65K 
[   ]chr5.subst.fa.gz09-Sep-2015 13:26 64M 
[   ]chr6.subst.fa.gz09-Sep-2015 13:26 60M 
[   ]chr6_apd_hap1.subst.fa.gz09-Sep-2015 13:26 784K 
[   ]chr6_cox_hap2.subst.fa.gz09-Sep-2015 13:26 1.5M 
[   ]chr6_dbb_hap3.subst.fa.gz09-Sep-2015 13:26 1.3M 
[   ]chr6_mann_hap4.subst.fa.gz09-Sep-2015 13:26 1.3M 
[   ]chr6_mcf_hap5.subst.fa.gz09-Sep-2015 13:26 1.2M 
[   ]chr6_qbl_hap6.subst.fa.gz09-Sep-2015 13:26 1.4M 
[   ]chr6_ssto_hap7.subst.fa.gz09-Sep-2015 13:26 1.3M 
[   ]chr7.subst.fa.gz09-Sep-2015 13:26 55M 
[   ]chr7_gl000195_random.subst.fa.gz09-Sep-2015 13:26 66K 
[   ]chr8.subst.fa.gz09-Sep-2015 13:26 52M 
[   ]chr8_gl000196_random.subst.fa.gz09-Sep-2015 13:26 13K 
[   ]chr8_gl000197_random.subst.fa.gz09-Sep-2015 13:26 12K 
[   ]chr9.subst.fa.gz09-Sep-2015 13:26 43M 
[   ]chr9_gl000198_random.subst.fa.gz09-Sep-2015 13:26 20K 
[   ]chr9_gl000199_random.subst.fa.gz09-Sep-2015 13:26 28K 
[   ]chr9_gl000200_random.subst.fa.gz09-Sep-2015 13:26 61K 
[   ]chr9_gl000201_random.subst.fa.gz09-Sep-2015 13:26 12K 
[   ]chr10.subst.fa.gz09-Sep-2015 13:23 47M 
[   ]chr11.subst.fa.gz09-Sep-2015 13:23 47M 
[   ]chr11_gl000202_random.subst.fa.gz09-Sep-2015 13:23 13K 
[   ]chr12.subst.fa.gz09-Sep-2015 13:23 47M 
[   ]chr13.subst.fa.gz09-Sep-2015 13:23 34M 
[   ]chr14.subst.fa.gz09-Sep-2015 13:24 32M 
[   ]chr15.subst.fa.gz09-Sep-2015 13:24 29M 
[   ]chr16.subst.fa.gz09-Sep-2015 13:24 29M 
[   ]chr17.subst.fa.gz09-Sep-2015 13:24 28M 
[   ]chr17_ctg5_hap1.subst.fa.gz09-Sep-2015 13:24 520K 
[   ]chr17_gl000203_random.subst.fa.gz09-Sep-2015 13:24 13K 
[   ]chr17_gl000204_random.subst.fa.gz09-Sep-2015 13:24 27K 
[   ]chr17_gl000205_random.subst.fa.gz09-Sep-2015 13:24 57K 
[   ]chr17_gl000206_random.subst.fa.gz09-Sep-2015 13:24 13K 
[   ]chr18.subst.fa.gz09-Sep-2015 13:24 27M 
[   ]chr18_gl000207_random.subst.fa.gz09-Sep-2015 13:24 1.5K 
[   ]chr19.subst.fa.gz09-Sep-2015 13:24 20M 
[   ]chr19_gl000208_random.subst.fa.gz09-Sep-2015 13:24 24K 
[   ]chr19_gl000209_random.subst.fa.gz09-Sep-2015 13:24 48K 
[   ]chr20.subst.fa.gz09-Sep-2015 13:25 21M 
[   ]chr21.subst.fa.gz09-Sep-2015 13:25 13M 
[   ]chr21_gl000210_random.subst.fa.gz09-Sep-2015 13:25 9.0K 
[   ]chr22.subst.fa.gz09-Sep-2015 13:25 13M 
[   ]chrM.subst.fa.gz09-Sep-2015 13:27 6.5K 
[   ]chrUn_gl000211.subst.fa.gz09-Sep-2015 13:26 56K 
[   ]chrUn_gl000212.subst.fa.gz09-Sep-2015 13:26 62K 
[   ]chrUn_gl000213.subst.fa.gz09-Sep-2015 13:26 53K 
[   ]chrUn_gl000214.subst.fa.gz09-Sep-2015 13:26 43K 
[   ]chrUn_gl000215.subst.fa.gz09-Sep-2015 13:26 56K 
[   ]chrUn_gl000216.subst.fa.gz09-Sep-2015 13:26 43K 
[   ]chrUn_gl000217.subst.fa.gz09-Sep-2015 13:26 56K 
[   ]chrUn_gl000218.subst.fa.gz09-Sep-2015 13:26 56K 
[   ]chrUn_gl000219.subst.fa.gz09-Sep-2015 13:26 59K 
[   ]chrUn_gl000220.subst.fa.gz09-Sep-2015 13:26 54K 
[   ]chrUn_gl000221.subst.fa.gz09-Sep-2015 13:26 52K 
[   ]chrUn_gl000222.subst.fa.gz09-Sep-2015 13:26 60K 
[   ]chrUn_gl000223.subst.fa.gz09-Sep-2015 13:26 57K 
[   ]chrUn_gl000224.subst.fa.gz09-Sep-2015 13:26 51K 
[   ]chrUn_gl000225.subst.fa.gz09-Sep-2015 13:26 58K 
[   ]chrUn_gl000226.subst.fa.gz09-Sep-2015 13:26 2.6K 
[   ]chrUn_gl000227.subst.fa.gz09-Sep-2015 13:26 41K 
[   ]chrUn_gl000228.subst.fa.gz09-Sep-2015 13:26 33K 
[   ]chrUn_gl000229.subst.fa.gz09-Sep-2015 13:26 6.7K 
[   ]chrUn_gl000230.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000231.subst.fa.gz09-Sep-2015 13:26 9.4K 
[   ]chrUn_gl000232.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000233.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000234.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000235.subst.fa.gz09-Sep-2015 13:26 12K 
[   ]chrUn_gl000236.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000237.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000238.subst.fa.gz09-Sep-2015 13:26 13K 
[   ]chrUn_gl000239.subst.fa.gz09-Sep-2015 13:26 11K 
[   ]chrUn_gl000240.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000241.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000243.subst.fa.gz09-Sep-2015 13:26 14K 
[   ]chrUn_gl000244.subst.fa.gz09-Sep-2015 13:26 13K 
[   ]chrUn_gl000245.subst.fa.gz09-Sep-2015 13:26 12K 
[   ]chrUn_gl000246.subst.fa.gz09-Sep-2015 13:26 13K 
[   ]chrUn_gl000247.subst.fa.gz09-Sep-2015 13:27 12K 
[   ]chrUn_gl000248.subst.fa.gz09-Sep-2015 13:27 13K 
[   ]chrX.subst.fa.gz09-Sep-2015 13:27 51M 
[   ]chrY.subst.fa.gz09-Sep-2015 13:27 8.3M 
[TXT]md5sum.txt09-Sep-2015 13:43 5.3K 

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