This directory contains FASTA files which contain a modified version
of the Genome Reference Consortium human genome build 37 (hg19, Feb. 2009). 
The chromosomal sequences were assembled by the International Human 
Genome Project sequencing centers.  The hg19/GRCh37 assembly 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 142.  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.snp142 database table as well as the
  hg19.snp142ExceptionDesc 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/snp142Mask/ .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp142Mask/chr1.subst.fa.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp142Mask/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp142Mask/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.txt05-Nov-2014 15:49 2.6K 
[   ]chr1.subst.fa.gz05-Nov-2014 12:49 79M 
[   ]chr1_gl000191_random.subst.fa.gz05-Nov-2014 12:50 33K 
[   ]chr1_gl000192_random.subst.fa.gz05-Nov-2014 12:50 178K 
[   ]chr2.subst.fa.gz05-Nov-2014 12:50 84M 
[   ]chr3.subst.fa.gz05-Nov-2014 12:50 69M 
[   ]chr4.subst.fa.gz05-Nov-2014 12:50 66M 
[   ]chr4_ctg9_hap1.subst.fa.gz05-Nov-2014 12:50 215K 
[   ]chr4_gl000193_random.subst.fa.gz05-Nov-2014 12:51 61K 
[   ]chr4_gl000194_random.subst.fa.gz05-Nov-2014 12:51 65K 
[   ]chr5.subst.fa.gz05-Nov-2014 12:51 62M 
[   ]chr6.subst.fa.gz05-Nov-2014 12:51 59M 
[   ]chr6_apd_hap1.subst.fa.gz05-Nov-2014 12:51 864K 
[   ]chr6_cox_hap2.subst.fa.gz05-Nov-2014 12:51 1.7M 
[   ]chr6_dbb_hap3.subst.fa.gz05-Nov-2014 12:51 1.5M 
[   ]chr6_mann_hap4.subst.fa.gz05-Nov-2014 12:51 1.5M 
[   ]chr6_mcf_hap5.subst.fa.gz05-Nov-2014 12:51 1.4M 
[   ]chr6_qbl_hap6.subst.fa.gz05-Nov-2014 12:51 1.5M 
[   ]chr6_ssto_hap7.subst.fa.gz05-Nov-2014 12:51 1.5M 
[   ]chr7.subst.fa.gz05-Nov-2014 12:51 54M 
[   ]chr7_gl000195_random.subst.fa.gz05-Nov-2014 12:51 66K 
[   ]chr8.subst.fa.gz05-Nov-2014 12:51 51M 
[   ]chr8_gl000196_random.subst.fa.gz05-Nov-2014 12:51 13K 
[   ]chr8_gl000197_random.subst.fa.gz05-Nov-2014 12:51 12K 
[   ]chr9.subst.fa.gz05-Nov-2014 12:51 42M 
[   ]chr9_gl000198_random.subst.fa.gz05-Nov-2014 12:51 20K 
[   ]chr9_gl000199_random.subst.fa.gz05-Nov-2014 12:51 31K 
[   ]chr9_gl000200_random.subst.fa.gz05-Nov-2014 12:51 61K 
[   ]chr9_gl000201_random.subst.fa.gz05-Nov-2014 12:51 12K 
[   ]chr10.subst.fa.gz05-Nov-2014 12:49 46M 
[   ]chr11.subst.fa.gz05-Nov-2014 12:49 46M 
[   ]chr11_gl000202_random.subst.fa.gz05-Nov-2014 12:49 13K 
[   ]chr12.subst.fa.gz05-Nov-2014 12:49 46M 
[   ]chr13.subst.fa.gz05-Nov-2014 12:49 34M 
[   ]chr14.subst.fa.gz05-Nov-2014 12:49 31M 
[   ]chr15.subst.fa.gz05-Nov-2014 12:49 29M 
[   ]chr16.subst.fa.gz05-Nov-2014 12:49 28M 
[   ]chr17.subst.fa.gz05-Nov-2014 12:49 27M 
[   ]chr17_ctg5_hap1.subst.fa.gz05-Nov-2014 12:49 544K 
[   ]chr17_gl000203_random.subst.fa.gz05-Nov-2014 12:49 13K 
[   ]chr17_gl000204_random.subst.fa.gz05-Nov-2014 12:49 27K 
[   ]chr17_gl000205_random.subst.fa.gz05-Nov-2014 12:49 58K 
[   ]chr17_gl000206_random.subst.fa.gz05-Nov-2014 12:50 13K 
[   ]chr18.subst.fa.gz05-Nov-2014 12:50 26M 
[   ]chr18_gl000207_random.subst.fa.gz05-Nov-2014 12:50 1.5K 
[   ]chr19.subst.fa.gz05-Nov-2014 12:50 19M 
[   ]chr19_gl000208_random.subst.fa.gz05-Nov-2014 12:50 24K 
[   ]chr19_gl000209_random.subst.fa.gz05-Nov-2014 12:50 47K 
[   ]chr20.subst.fa.gz05-Nov-2014 12:50 21M 
[   ]chr21.subst.fa.gz05-Nov-2014 12:50 12M 
[   ]chr21_gl000210_random.subst.fa.gz05-Nov-2014 12:50 9.0K 
[   ]chr22.subst.fa.gz05-Nov-2014 12:50 12M 
[   ]chrM.subst.fa.gz05-Nov-2014 12:51 6.5K 
[   ]chrUn_gl000211.subst.fa.gz05-Nov-2014 12:51 56K 
[   ]chrUn_gl000212.subst.fa.gz05-Nov-2014 12:51 62K 
[   ]chrUn_gl000213.subst.fa.gz05-Nov-2014 12:51 53K 
[   ]chrUn_gl000214.subst.fa.gz05-Nov-2014 12:51 44K 
[   ]chrUn_gl000215.subst.fa.gz05-Nov-2014 12:51 56K 
[   ]chrUn_gl000216.subst.fa.gz05-Nov-2014 12:51 43K 
[   ]chrUn_gl000217.subst.fa.gz05-Nov-2014 12:51 56K 
[   ]chrUn_gl000218.subst.fa.gz05-Nov-2014 12:51 56K 
[   ]chrUn_gl000219.subst.fa.gz05-Nov-2014 12:51 59K 
[   ]chrUn_gl000220.subst.fa.gz05-Nov-2014 12:51 54K 
[   ]chrUn_gl000221.subst.fa.gz05-Nov-2014 12:51 51K 
[   ]chrUn_gl000222.subst.fa.gz05-Nov-2014 12:51 60K 
[   ]chrUn_gl000223.subst.fa.gz05-Nov-2014 12:51 57K 
[   ]chrUn_gl000224.subst.fa.gz05-Nov-2014 12:51 52K 
[   ]chrUn_gl000225.subst.fa.gz05-Nov-2014 12:51 58K 
[   ]chrUn_gl000226.subst.fa.gz05-Nov-2014 12:51 3.5K 
[   ]chrUn_gl000227.subst.fa.gz05-Nov-2014 12:51 41K 
[   ]chrUn_gl000228.subst.fa.gz05-Nov-2014 12:51 33K 
[   ]chrUn_gl000229.subst.fa.gz05-Nov-2014 12:51 6.7K 
[   ]chrUn_gl000230.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000231.subst.fa.gz05-Nov-2014 12:51 9.4K 
[   ]chrUn_gl000232.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000233.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000234.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000235.subst.fa.gz05-Nov-2014 12:51 12K 
[   ]chrUn_gl000236.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000237.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000238.subst.fa.gz05-Nov-2014 12:51 13K 
[   ]chrUn_gl000239.subst.fa.gz05-Nov-2014 12:51 11K 
[   ]chrUn_gl000240.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000241.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000243.subst.fa.gz05-Nov-2014 12:51 14K 
[   ]chrUn_gl000244.subst.fa.gz05-Nov-2014 12:51 13K 
[   ]chrUn_gl000245.subst.fa.gz05-Nov-2014 12:51 12K 
[   ]chrUn_gl000246.subst.fa.gz05-Nov-2014 12:51 13K 
[   ]chrUn_gl000247.subst.fa.gz05-Nov-2014 12:51 12K 
[   ]chrUn_gl000248.subst.fa.gz05-Nov-2014 12:51 13K 
[   ]chrX.subst.fa.gz05-Nov-2014 12:51 50M 
[   ]chrY.subst.fa.gz05-Nov-2014 12:51 8.1M 
[TXT]md5sum.txt05-Nov-2014 15:49 5.3K 

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