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 135.  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.snp135 database table as well as the
  hg19.snp135ExceptionDesc 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 

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
[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:// .
For a single file, e.g. chr1.subst.fa.gz
    rsync -avzP \
        rsync:// .

Or with wget, all files:
    wget --timestamping \
With wget, a single file:
    wget --timestamping \
        '' \
        -O chr1.subst.fa.gz

To uncompress the fa.gz files:
    gunzip <file>.fa.gz

      Name                        Last modified      Size  Description
Parent Directory - md5sum.txt 2011-11-14 14:47 1.8K chrM.subst.fa.gz 2011-11-14 14:33 6.1K chr4_ctg9_hap1.subst.fa.gz 2011-11-14 14:31 196K chr17_ctg5_hap1.subst.fa.gz 2011-11-14 14:25 512K chr6_apd_hap1.subst.fa.gz 2011-11-14 14:31 803K chr6_mcf_hap5.subst.fa.gz 2011-11-14 14:31 1.3M chr6_mann_hap4.subst.fa.gz 2011-11-14 14:31 1.3M chr6_dbb_hap3.subst.fa.gz 2011-11-14 14:31 1.4M chr6_ssto_hap7.subst.fa.gz 2011-11-14 14:32 1.4M chr6_qbl_hap6.subst.fa.gz 2011-11-14 14:32 1.4M chr6_cox_hap2.subst.fa.gz 2011-11-14 14:31 1.6M chrY.subst.fa.gz 2011-11-14 14:33 8.0M chr22.subst.fa.gz 2011-11-14 14:30 12M chr21.subst.fa.gz 2011-11-14 14:29 12M chr19.subst.fa.gz 2011-11-14 14:27 18M chr20.subst.fa.gz 2011-11-14 14:28 20M chr18.subst.fa.gz 2011-11-14 14:27 25M chr17.subst.fa.gz 2011-11-14 14:25 26M chr16.subst.fa.gz 2011-11-14 14:25 26M chr15.subst.fa.gz 2011-11-14 14:25 27M chr14.subst.fa.gz 2011-11-14 14:25 29M chr13.subst.fa.gz 2011-11-14 14:24 32M chr9.subst.fa.gz 2011-11-14 14:32 40M chr12.subst.fa.gz 2011-11-14 14:24 43M chr11.subst.fa.gz 2011-11-14 14:23 44M chr10.subst.fa.gz 2011-11-14 14:23 44M chr8.subst.fa.gz 2011-11-14 14:32 48M chrX.subst.fa.gz 2011-11-14 14:33 49M chr7.subst.fa.gz 2011-11-14 14:32 51M chr6.subst.fa.gz 2011-11-14 14:31 56M chr5.subst.fa.gz 2011-11-14 14:31 59M chr4.subst.fa.gz 2011-11-14 14:31 63M chr3.subst.fa.gz 2011-11-14 14:30 65M chr1.subst.fa.gz 2011-11-14 14:22 75M chr2.subst.fa.gz 2011-11-14 14:27 79M