This directory contains FASTA files which contain a modified version
of the Build 36.1 finished human genome assembly (hg18,
Mar. 2006). The chromosomal sequences were assembled by the
International Human Genome Project sequencing centers. The hg18/36.1
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 129. 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
- UCSC tagged the dbSNP item with any of these exceptions (see also
hg18.snp129Exceptions and hg18.snp129ExceptionDesc database tables):
- MultipleAlignments: dbSNP mapped item to multiple locations
- ObservedMismatch: the reference allele does not appear in the item's
- ObservedWrongFormat: the observed sequence has an unexpected format
(no instances of this exception were found in snp129)
- 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 hgdownload.cse.ucsc.edu
[username: anonymous, password: your email address], then cd to the
directory goldenPath/hg18/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/hg18/snp129Mask/ .
For a single file, e.g. chr1.subst.fa.gz
rsync -avzP \
Or with wget, all files:
wget --timestamping \
With wget, a single file:
wget --timestamping \
To uncompress the fa.gz files:
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80