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 - chr1.fa.gz 20-Mar-2009 08:58 70M chr1_gl000191_random.fa.gz 20-Mar-2009 09:02 33K chr1_gl000192_random.fa.gz 20-Mar-2009 09:02 178K chr2.fa.gz 20-Mar-2009 08:58 75M chr3.fa.gz 20-Mar-2009 08:58 61M chr4.fa.gz 20-Mar-2009 08:59 59M chr4_ctg9_hap1.fa.gz 20-Mar-2009 09:02 190K chr4_gl000193_random.fa.gz 20-Mar-2009 09:02 57K chr4_gl000194_random.fa.gz 20-Mar-2009 09:02 61K chr5.fa.gz 20-Mar-2009 08:59 56M chr6.fa.gz 20-Mar-2009 08:59 52M chr6_apd_hap1.fa.gz 20-Mar-2009 09:02 768K chr6_cox_hap2.fa.gz 20-Mar-2009 09:02 1.5M chr6_dbb_hap3.fa.gz 20-Mar-2009 09:02 1.3M chr6_mann_hap4.fa.gz 20-Mar-2009 09:02 1.3M chr6_mcf_hap5.fa.gz 20-Mar-2009 09:02 1.2M chr6_qbl_hap6.fa.gz 20-Mar-2009 09:02 1.3M chr6_ssto_hap7.fa.gz 20-Mar-2009 09:02 1.3M chr7.fa.gz 20-Mar-2009 08:59 48M chr7_gl000195_random.fa.gz 20-Mar-2009 09:02 60K chr8.fa.gz 20-Mar-2009 09:00 45M chr8_gl000196_random.fa.gz 20-Mar-2009 09:02 13K chr8_gl000197_random.fa.gz 20-Mar-2009 09:02 12K chr9.fa.gz 20-Mar-2009 09:00 38M chr9_gl000198_random.fa.gz 20-Mar-2009 09:02 18K chr9_gl000199_random.fa.gz 20-Mar-2009 09:02 24K chr9_gl000200_random.fa.gz 20-Mar-2009 09:02 61K chr9_gl000201_random.fa.gz 20-Mar-2009 09:02 12K chr10.fa.gz 20-Mar-2009 09:00 41M chr11.fa.gz 20-Mar-2009 09:00 41M chr11_gl000202_random.fa.gz 20-Mar-2009 09:02 13K chr12.fa.gz 20-Mar-2009 09:01 41M chr13.fa.gz 20-Mar-2009 09:01 30M chr14.fa.gz 20-Mar-2009 09:01 28M chr15.fa.gz 20-Mar-2009 09:01 26M chr16.fa.gz 20-Mar-2009 09:01 24M chr17.fa.gz 20-Mar-2009 09:01 24M chr17_ctg5_hap1.fa.gz 20-Mar-2009 09:02 501K chr17_gl000203_random.fa.gz 20-Mar-2009 09:02 13K chr17_gl000204_random.fa.gz 20-Mar-2009 09:02 26K chr17_gl000205_random.fa.gz 20-Mar-2009 09:02 53K chr17_gl000206_random.fa.gz 20-Mar-2009 09:02 13K chr18.fa.gz 20-Mar-2009 09:01 23M chr18_gl000207_random.fa.gz 20-Mar-2009 09:02 1.4K chr19.fa.gz 20-Mar-2009 09:02 17M chr19_gl000208_random.fa.gz 20-Mar-2009 09:02 21K chr19_gl000209_random.fa.gz 20-Mar-2009 09:02 47K chr20.fa.gz 20-Mar-2009 09:02 19M chr21.fa.gz 20-Mar-2009 09:02 11M chr21_gl000210_random.fa.gz 20-Mar-2009 09:02 9.0K chr22.fa.gz 20-Mar-2009 09:02 11M chrM.fa.gz 20-Mar-2009 09:02 5.4K chrUn_gl000211.fa.gz 20-Mar-2009 09:02 54K chrUn_gl000212.fa.gz 20-Mar-2009 09:02 60K chrUn_gl000213.fa.gz 20-Mar-2009 09:02 53K chrUn_gl000214.fa.gz 20-Mar-2009 09:02 41K chrUn_gl000215.fa.gz 20-Mar-2009 09:02 56K chrUn_gl000216.fa.gz 20-Mar-2009 09:02 42K chrUn_gl000217.fa.gz 20-Mar-2009 09:02 55K chrUn_gl000218.fa.gz 20-Mar-2009 09:02 52K chrUn_gl000219.fa.gz 20-Mar-2009 09:02 56K chrUn_gl000220.fa.gz 20-Mar-2009 09:02 51K chrUn_gl000221.fa.gz 20-Mar-2009 09:02 50K chrUn_gl000222.fa.gz 20-Mar-2009 09:02 60K chrUn_gl000223.fa.gz 20-Mar-2009 09:02 57K chrUn_gl000224.fa.gz 20-Mar-2009 09:02 49K chrUn_gl000225.fa.gz 20-Mar-2009 09:02 56K chrUn_gl000226.fa.gz 20-Mar-2009 09:02 1.9K chrUn_gl000227.fa.gz 20-Mar-2009 09:02 41K chrUn_gl000228.fa.gz 20-Mar-2009 09:02 33K chrUn_gl000229.fa.gz 20-Mar-2009 09:02 6.6K chrUn_gl000230.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000231.fa.gz 20-Mar-2009 09:02 9.2K chrUn_gl000232.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000233.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000234.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000235.fa.gz 20-Mar-2009 09:02 12K chrUn_gl000236.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000237.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000238.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000239.fa.gz 20-Mar-2009 09:02 10K chrUn_gl000240.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000241.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000242.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000243.fa.gz 20-Mar-2009 09:02 14K chrUn_gl000244.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000245.fa.gz 20-Mar-2009 09:02 12K chrUn_gl000246.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000247.fa.gz 20-Mar-2009 09:02 11K chrUn_gl000248.fa.gz 20-Mar-2009 09:02 13K chrUn_gl000249.fa.gz 20-Mar-2009 09:02 13K chrX.fa.gz 20-Mar-2009 09:00 47M chrY.fa.gz 20-Mar-2009 09:02 7.9M md5sum.txt 20-Mar-2009 09:49 4.9K