This directory contains the Feb. 2009 assembly of the human genome (hg19,
GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))
in one gzip-compressed FASTA file per chromosome.
The Feb. 2009 human reference sequence (GRCh37) was produced by the
Genome Reference Consortium:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
Note on chrM:
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion
sequence (represented as "chrM" in the Genome Browser) has been replaced in
GenBank with the record NC_012920. We have not replaced the original sequence,
NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge
Reference Sequence (rCRS, http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq)
in the next human assembly release.
Files included in this directory:
- chr*.fa.gz: compressed FASTA sequence of each chromosome.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
RepeatMasker was run with the -s (sensitive) setting.
Using: Jan 29 2009 (open-3-2-7) version of RepeatMasker and
RELEASE 20090120 of library RepeatMaskerLib.embl
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See also: Wellcome Trust Sanger Institute MHC Haplotype Project
for additional information on the chr6 alternate haplotype assemblies:
http://www.sanger.ac.uk/HGP/Chr6/MHC/
The chr*_random sequences are unplaced sequence on those reference
chromosomes.
The chrUn_* sequences are unlocalized sequences where the corresponding
reference chromosome has not been determined.
See also: NCBI discussion of assembly procedures:
http://www.ncbi.nlm.nih.gov/genome/assembly/assembly.shtml
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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, then
go to the directory goldenPath/hg19/chromosomes. 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/chromosomes/ .
For a single file, e.g. chrM.fa.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrM.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrM.fa.gz'
-O chrM.fa.gz
To uncompress the fa.gz files:
gunzip <file>.fa.gz
All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory -
md5sum.txt 2009-03-20 09:49 4.9K
chrY.fa.gz 2009-03-20 09:02 7.9M
chrX.fa.gz 2009-03-20 09:00 47M
chrUn_gl000249.fa.gz 2009-03-20 09:02 13K
chrUn_gl000248.fa.gz 2009-03-20 09:02 13K
chrUn_gl000247.fa.gz 2009-03-20 09:02 11K
chrUn_gl000246.fa.gz 2009-03-20 09:02 13K
chrUn_gl000245.fa.gz 2009-03-20 09:02 12K
chrUn_gl000244.fa.gz 2009-03-20 09:02 13K
chrUn_gl000243.fa.gz 2009-03-20 09:02 14K
chrUn_gl000242.fa.gz 2009-03-20 09:02 14K
chrUn_gl000241.fa.gz 2009-03-20 09:02 14K
chrUn_gl000240.fa.gz 2009-03-20 09:02 13K
chrUn_gl000239.fa.gz 2009-03-20 09:02 10K
chrUn_gl000238.fa.gz 2009-03-20 09:02 13K
chrUn_gl000237.fa.gz 2009-03-20 09:02 14K
chrUn_gl000236.fa.gz 2009-03-20 09:02 14K
chrUn_gl000235.fa.gz 2009-03-20 09:02 12K
chrUn_gl000234.fa.gz 2009-03-20 09:02 14K
chrUn_gl000233.fa.gz 2009-03-20 09:02 13K
chrUn_gl000232.fa.gz 2009-03-20 09:02 14K
chrUn_gl000231.fa.gz 2009-03-20 09:02 9.2K
chrUn_gl000230.fa.gz 2009-03-20 09:02 13K
chrUn_gl000229.fa.gz 2009-03-20 09:02 6.6K
chrUn_gl000228.fa.gz 2009-03-20 09:02 33K
chrUn_gl000227.fa.gz 2009-03-20 09:02 41K
chrUn_gl000226.fa.gz 2009-03-20 09:02 1.9K
chrUn_gl000225.fa.gz 2009-03-20 09:02 56K
chrUn_gl000224.fa.gz 2009-03-20 09:02 49K
chrUn_gl000223.fa.gz 2009-03-20 09:02 57K
chrUn_gl000222.fa.gz 2009-03-20 09:02 60K
chrUn_gl000221.fa.gz 2009-03-20 09:02 50K
chrUn_gl000220.fa.gz 2009-03-20 09:02 51K
chrUn_gl000219.fa.gz 2009-03-20 09:02 56K
chrUn_gl000218.fa.gz 2009-03-20 09:02 52K
chrUn_gl000217.fa.gz 2009-03-20 09:02 55K
chrUn_gl000216.fa.gz 2009-03-20 09:02 42K
chrUn_gl000215.fa.gz 2009-03-20 09:02 56K
chrUn_gl000214.fa.gz 2009-03-20 09:02 41K
chrUn_gl000213.fa.gz 2009-03-20 09:02 53K
chrUn_gl000212.fa.gz 2009-03-20 09:02 60K
chrUn_gl000211.fa.gz 2009-03-20 09:02 54K
chrM.fa.gz 2009-03-20 09:02 5.4K
chr22.fa.gz 2009-03-20 09:02 11M
chr21_gl000210_random.fa.gz 2009-03-20 09:02 9.0K
chr21.fa.gz 2009-03-20 09:02 11M
chr20.fa.gz 2009-03-20 09:02 19M
chr19_gl000209_random.fa.gz 2009-03-20 09:02 47K
chr19_gl000208_random.fa.gz 2009-03-20 09:02 21K
chr19.fa.gz 2009-03-20 09:02 17M
chr18_gl000207_random.fa.gz 2009-03-20 09:02 1.4K
chr18.fa.gz 2009-03-20 09:01 23M
chr17_gl000206_random.fa.gz 2009-03-20 09:02 13K
chr17_gl000205_random.fa.gz 2009-03-20 09:02 53K
chr17_gl000204_random.fa.gz 2009-03-20 09:02 26K
chr17_gl000203_random.fa.gz 2009-03-20 09:02 13K
chr17_ctg5_hap1.fa.gz 2009-03-20 09:02 501K
chr17.fa.gz 2009-03-20 09:01 24M
chr16.fa.gz 2009-03-20 09:01 24M
chr15.fa.gz 2009-03-20 09:01 26M
chr14.fa.gz 2009-03-20 09:01 28M
chr13.fa.gz 2009-03-20 09:01 30M
chr12.fa.gz 2009-03-20 09:01 41M
chr11_gl000202_random.fa.gz 2009-03-20 09:02 13K
chr11.fa.gz 2009-03-20 09:00 41M
chr10.fa.gz 2009-03-20 09:00 41M
chr9_gl000201_random.fa.gz 2009-03-20 09:02 12K
chr9_gl000200_random.fa.gz 2009-03-20 09:02 61K
chr9_gl000199_random.fa.gz 2009-03-20 09:02 24K
chr9_gl000198_random.fa.gz 2009-03-20 09:02 18K
chr9.fa.gz 2009-03-20 09:00 38M
chr8_gl000197_random.fa.gz 2009-03-20 09:02 12K
chr8_gl000196_random.fa.gz 2009-03-20 09:02 13K
chr8.fa.gz 2009-03-20 09:00 45M
chr7_gl000195_random.fa.gz 2009-03-20 09:02 60K
chr7.fa.gz 2009-03-20 08:59 48M
chr6_ssto_hap7.fa.gz 2009-03-20 09:02 1.3M
chr6_qbl_hap6.fa.gz 2009-03-20 09:02 1.3M
chr6_mcf_hap5.fa.gz 2009-03-20 09:02 1.2M
chr6_mann_hap4.fa.gz 2009-03-20 09:02 1.3M
chr6_dbb_hap3.fa.gz 2009-03-20 09:02 1.3M
chr6_cox_hap2.fa.gz 2009-03-20 09:02 1.5M
chr6_apd_hap1.fa.gz 2009-03-20 09:02 768K
chr6.fa.gz 2009-03-20 08:59 52M
chr5.fa.gz 2009-03-20 08:59 56M
chr4_gl000194_random.fa.gz 2009-03-20 09:02 61K
chr4_gl000193_random.fa.gz 2009-03-20 09:02 57K
chr4_ctg9_hap1.fa.gz 2009-03-20 09:02 190K
chr4.fa.gz 2009-03-20 08:59 59M
chr3.fa.gz 2009-03-20 08:58 61M
chr2.fa.gz 2009-03-20 08:58 75M
chr1_gl000192_random.fa.gz 2009-03-20 09:02 178K
chr1_gl000191_random.fa.gz 2009-03-20 09:02 33K
chr1.fa.gz 2009-03-20 08:58 70M