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