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.
Name Last modified Size Description
Parent Directory -
chromFa.zip 2003-04-12 19:18 895M
contigFa.zip 2003-04-12 19:20 894M
chromFaMasked.zip 2003-04-12 19:19 489M
contigFaMasked.zip 2003-04-12 19:20 489M
chromOut.zip 2003-04-12 02:52 150M
contigOut.zip 2003-04-12 04:27 149M
upstream5000.fa 2003-07-08 13:29 86M
mrna.zip 2003-05-09 22:56 59M
upstream2000.fa 2003-07-08 13:29 35M
upstream5000.zip 2003-07-08 13:31 23M
upstream1000.fa 2003-07-08 13:29 18M
upstream2000.zip 2003-07-08 13:30 9.6M
contigTrf.zip 2003-04-12 05:58 7.0M
chromTrf.zip 2003-04-12 05:57 6.7M
upstream1000.zip 2003-07-08 13:29 5.0M
contigAgp.zip 2003-04-18 12:34 616K
chromAgp.zip 2003-04-18 12:33 530K
liftAll.zip 2003-04-16 14:10 7.8K
bak/ 2003-04-16 14:11 -