This directory contains the first finished human genome
assembly, dated April 2003 (hg15). The chromosomal sequences were 
assembled by the International Human Genome Project sequencing 
centers and verified by NCBI and UCSC. The annotations are from 
UCSC and collaborators worldwide.

Files included in this directory:

chromAgp.zip - Description of how the assembly was generated from
    fragments. Similar to contigAgp.zip, but unpacks to one 
    file per chromosome.  

chromFa.zip - The reference sequence chromosome in one file per
    chromosome.  Repeats from RepeatMasker and Tandem Repeats Finder
    (with period of 12 or less) are in lower case while non-repeating
    sequence is in upper case.  The main assembly is in the chrN.fa
    files where N is the name of the chromosome.  The chrN_random.fa
    files contain clones which are either not yet finished, or which
    cannot be placed with certainty at a specific place on the
    chromosome. In some cases including the human HLA region on
    chromosome 6, the chrN_random.fa files also contain different
    haplotypes than the main assembly.

chromFaMasked.zip - The reference  sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

chromOut.zip - RepeatMasker .out file for chromosomes.  These were 
    created with RepeatMasker at the -s sensitive setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per chromosomes.  

contigAgp.zip - Description of how the assembly was generated 
    from fragments at a contig layout level. 

contigFa.zip - The reference sequence one file per NCBI contig.
    All contigs are in forward orientation relative to the chromosome,
    which means that some will be reversed relative to their
    orientation in the NCBI assembly. Repeats from RepeatMasker and
    Tandem Repeats Finder (with period of 12 or less) are in lower
    case while non-repeating sequence is in upper case.

contigFaMasked.zip - the reference sequence contigs,
    in one file per contig. Repeats are masked by capital Ns and
    non-repeating sequence is shown in upper case.  

contigOut.zip - RepeatMasker .out file for contigs.  These were 
    created with RepeatMasker at the -s sensitive setting.

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, translated into one .bed file 
    per contig.  

liftAll.zip - A file that contains the offsets of contigs within
    chromosomes.

liftOver.zip - Contains a file that maps the previous assembly to this one.
    Use this in conjunction with the liftOver utility.

mrna.zip - A zipped-up file of human mRNA from GenBank.    

upstream1000.zip - Sequences 1000 bases upstream of annotated
    transcription start of RefSeq genes.  This only includes
    cases where the transcription start is annotated separately
    from the coding region start.

upstream2000.zip - As above but 2000 bases.

upstream5000.zip - As above but 5000 bases.

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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/10april2003/bigZips. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the files in this directory are freely available for public use.