This directory contains a dump of the UCSC genome annotation database for
Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly of the pig
genome (susScr2, SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2)),
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Swine Genome Sequencing Consortium
and Wellcome Trust Sange Institute.
For more information on the pig genome, see the project website:
http://piggenome.org/
http://www.sanger.ac.uk/resources/
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=susScr2
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend 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/susScr2/database/. 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/susScr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql susScr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql susScr2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84
bigFiles.txt.gz 2024-11-17 03:14 87
grp.txt.gz 2014-03-02 04:14 208
chromInfo.txt.gz 2010-05-11 16:22 219
chrM_intronEst.txt.gz 2016-07-17 11:28 495
history.txt.gz 2010-05-11 16:45 567
hgFindSpec.txt.gz 2023-03-28 13:53 1.0K
ensPep.sql 2011-10-04 16:28 1.3K
ensemblSource.sql 2011-10-04 16:31 1.3K
bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K
chromInfo.sql 2010-05-11 16:22 1.3K
ensemblToGeneName.sql 2011-10-04 16:31 1.3K
grp.sql 2014-03-02 04:14 1.3K
ensGtp.sql 2011-10-04 16:28 1.4K
bigFiles.sql 2024-11-17 03:14 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
chainMm9Link.sql 2010-05-11 16:52 1.5K
chainHg19Link.sql 2010-05-11 16:47 1.5K
ctgPos2.sql 2010-05-11 16:59 1.5K
chainBosTau7Link.sql 2012-06-17 22:58 1.5K
chainMonDom5Link.sql 2010-05-11 16:55 1.5K
microsat.sql 2015-08-24 02:07 1.5K
history.sql 2010-05-11 16:45 1.5K
gap.sql 2010-05-11 16:55 1.5K
numtSMitochondrion.sql 2013-07-28 06:10 1.6K
tableList.sql 2024-11-17 03:14 1.6K
gold.sql 2010-05-11 16:52 1.6K
gbLoaded.sql 2020-09-02 07:33 1.6K
cpgIslandExt.sql 2010-05-11 16:43 1.6K
chainMm9.sql 2010-05-11 17:00 1.6K
chainHg19.sql 2010-05-11 17:01 1.6K
chainBosTau7.sql 2012-06-17 22:40 1.6K
chainMonDom5.sql 2010-05-11 16:59 1.6K
tRNAs.sql 2012-04-23 11:59 1.7K
gc5Base.sql 2010-05-11 16:51 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K
numtS.sql 2013-07-28 06:10 1.7K
xenoRefFlat.sql 2020-09-02 07:33 1.7K
hgFindSpec.sql 2023-03-28 13:53 1.8K
estOrientInfo.sql 2016-07-17 11:27 1.8K
rmsk.sql 2010-05-11 16:44 1.8K
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
numtSAssembled.sql 2013-07-28 06:10 1.8K
ensGene.sql 2011-10-04 16:28 1.9K
nscanGene.sql 2010-05-11 16:46 1.9K
simpleRepeat.sql 2010-05-11 16:44 1.9K
nestedRepeats.sql 2010-05-11 16:59 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
xenoRefGene.sql 2020-09-02 07:33 2.0K
netMm9.sql 2010-05-11 16:46 2.0K
netHg19.sql 2010-05-11 16:46 2.0K
netBosTau7.sql 2012-06-18 00:03 2.0K
netMonDom5.sql 2010-05-11 17:01 2.0K
blastHg18KG.sql 2010-05-11 17:01 2.1K
trackDb.sql 2023-03-28 13:53 2.1K
numtSAssembled.txt.gz 2013-07-28 06:10 2.1K
chr1_est.sql 2016-07-17 11:27 2.1K
chr2_est.sql 2016-07-17 11:28 2.1K
chr3_est.sql 2016-07-17 11:27 2.1K
chr4_est.sql 2016-07-17 11:27 2.1K
chr5_est.sql 2016-07-17 11:27 2.1K
chr6_est.sql 2016-07-17 11:27 2.1K
chr7_est.sql 2016-07-17 11:27 2.1K
chr8_est.sql 2016-07-17 11:27 2.1K
chr9_est.sql 2016-07-17 11:27 2.1K
chrM_est.sql 2016-07-17 11:27 2.1K
chrX_est.sql 2016-07-17 11:27 2.1K
chr10_est.sql 2016-07-17 11:27 2.1K
chr11_est.sql 2016-07-17 11:27 2.1K
chr12_est.sql 2016-07-17 11:28 2.1K
chr13_est.sql 2016-07-17 11:27 2.1K
chr14_est.sql 2016-07-17 11:27 2.1K
chr15_est.sql 2016-07-17 11:27 2.1K
chr16_est.sql 2016-07-17 11:27 2.1K
chr17_est.sql 2016-07-17 11:28 2.1K
chr18_est.sql 2016-07-17 11:25 2.1K
chrM_mrna.sql 2016-07-17 11:27 2.1K
all_est.sql 2016-07-17 11:28 2.1K
chr1_intronEst.sql 2016-07-17 11:28 2.1K
chr2_intronEst.sql 2016-07-17 11:27 2.1K
chr3_intronEst.sql 2016-07-17 11:27 2.1K
chr4_intronEst.sql 2016-07-17 11:27 2.1K
chr5_intronEst.sql 2016-07-17 11:25 2.1K
chr6_intronEst.sql 2016-07-17 11:27 2.1K
chr7_intronEst.sql 2016-07-17 11:27 2.1K
chr8_intronEst.sql 2016-07-17 11:28 2.1K
chr9_intronEst.sql 2016-07-17 11:27 2.1K
chrM_intronEst.sql 2016-07-17 11:28 2.1K
chrX_intronEst.sql 2016-07-17 11:27 2.1K
chr10_intronEst.sql 2016-07-17 11:28 2.1K
chr11_intronEst.sql 2016-07-17 11:28 2.1K
chr12_intronEst.sql 2016-07-17 11:28 2.1K
chr13_intronEst.sql 2016-07-17 11:27 2.1K
chr14_intronEst.sql 2016-07-17 11:28 2.1K
chr15_intronEst.sql 2016-07-17 11:28 2.1K
chr16_intronEst.sql 2016-07-17 11:28 2.1K
chr17_intronEst.sql 2016-07-17 11:28 2.1K
chr18_intronEst.sql 2016-07-17 11:27 2.1K
chr1_mrna.sql 2020-09-02 07:33 2.1K
chr2_mrna.sql 2020-05-11 17:36 2.1K
chr3_mrna.sql 2020-05-11 17:36 2.1K
chr4_mrna.sql 2020-09-02 07:33 2.1K
chr5_mrna.sql 2020-05-11 17:36 2.1K
chr6_mrna.sql 2020-05-11 17:36 2.1K
chr7_mrna.sql 2020-09-02 07:33 2.1K
chr8_mrna.sql 2020-05-11 17:36 2.1K
chr9_mrna.sql 2020-05-11 17:36 2.1K
chrX_mrna.sql 2020-05-11 17:36 2.1K
chr10_mrna.sql 2020-05-11 17:13 2.1K
chr11_mrna.sql 2020-05-11 17:13 2.1K
chr12_mrna.sql 2020-05-11 17:36 2.1K
chr13_mrna.sql 2020-09-02 07:33 2.1K
chr14_mrna.sql 2020-05-11 17:36 2.1K
chr15_mrna.sql 2020-05-11 17:36 2.1K
chr16_mrna.sql 2020-05-11 17:36 2.1K
chr17_mrna.sql 2020-05-11 17:36 2.1K
chr18_mrna.sql 2020-05-11 17:36 2.1K
all_mrna.sql 2020-09-02 07:33 2.1K
xenoMrna.sql 2020-09-02 07:33 2.1K
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K
chrM_mrna.txt.gz 2016-07-17 11:27 2.9K
tableDescriptions.txt.gz 2024-11-16 02:03 5.9K
tableList.txt.gz 2024-11-17 03:14 6.7K
numtS.txt.gz 2013-07-28 06:10 8.7K
tRNAs.txt.gz 2012-04-23 11:59 19K
trackDb.txt.gz 2023-03-28 13:53 36K
chr11_mrna.txt.gz 2020-05-11 17:13 40K
gbLoaded.txt.gz 2020-09-02 07:33 41K
chr16_mrna.txt.gz 2020-05-11 17:36 50K
ctgPos2.txt.gz 2010-05-11 16:59 53K
chr10_mrna.txt.gz 2020-05-11 17:13 60K
chr18_mrna.txt.gz 2020-05-11 17:36 62K
ensemblSource.txt.gz 2011-10-04 16:31 62K
chrX_mrna.txt.gz 2020-05-11 17:36 74K
chr17_mrna.txt.gz 2020-05-11 17:36 82K
chr8_mrna.txt.gz 2020-05-11 17:36 85K
chr15_mrna.txt.gz 2020-05-11 17:36 103K
chr12_mrna.txt.gz 2020-05-11 17:36 118K
ensemblToGeneName.txt.gz 2011-10-04 16:31 118K
chr9_mrna.txt.gz 2020-05-11 17:36 119K
chr13_mrna.txt.gz 2020-09-02 07:33 122K
chr5_mrna.txt.gz 2020-05-11 17:36 132K
chr3_mrna.txt.gz 2020-05-11 17:36 141K
chr4_mrna.txt.gz 2020-09-02 07:33 149K
chr14_mrna.txt.gz 2020-05-11 17:36 158K
ensGtp.txt.gz 2011-10-04 16:28 167K
chr6_mrna.txt.gz 2020-05-11 17:36 168K
chr2_mrna.txt.gz 2020-05-11 17:36 197K
chr1_mrna.txt.gz 2020-09-02 07:33 224K
chr7_mrna.txt.gz 2020-09-02 07:33 245K
microsat.txt.gz 2015-08-24 02:07 375K
chr11_intronEst.txt.gz 2016-07-17 11:28 379K
chr16_intronEst.txt.gz 2016-07-17 11:28 380K
chr18_intronEst.txt.gz 2016-07-17 11:27 466K
chr10_intronEst.txt.gz 2016-07-17 11:28 529K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K
cpgIslandExt.txt.gz 2010-05-11 16:43 805K
chrX_intronEst.txt.gz 2016-07-17 11:27 855K
chr11_est.txt.gz 2016-07-17 11:27 879K
chr16_est.txt.gz 2016-07-17 11:27 936K
chr17_intronEst.txt.gz 2016-07-17 11:28 950K
chr18_est.txt.gz 2016-07-17 11:25 1.0M
chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M
chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M
chrM_est.txt.gz 2016-07-17 11:27 1.1M
chr10_est.txt.gz 2016-07-17 11:27 1.1M
chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M
chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M
chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M
chr17_est.txt.gz 2016-07-17 11:28 1.6M
chrX_est.txt.gz 2016-07-17 11:27 1.7M
chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M
ensGene.txt.gz 2011-10-04 16:28 1.7M
chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M
chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M
nscanGene.txt.gz 2010-05-11 16:46 1.9M
chr8_est.txt.gz 2016-07-17 11:27 2.0M
augustusGene.txt.gz 2015-07-26 17:28 2.0M
chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M
gap.txt.gz 2010-05-11 16:55 2.1M
gold.txt.gz 2010-05-11 16:52 2.1M
chr15_est.txt.gz 2016-07-17 11:27 2.2M
chr12_est.txt.gz 2016-07-17 11:28 2.3M
chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M
all_mrna.txt.gz 2020-09-02 07:33 2.3M
chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr13_est.txt.gz 2016-07-17 11:27 2.4M
chr9_est.txt.gz 2016-07-17 11:27 2.6M
chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M
chr5_est.txt.gz 2016-07-17 11:27 3.2M
chr3_est.txt.gz 2016-07-17 11:27 3.2M
chr14_est.txt.gz 2016-07-17 11:27 3.5M
chr6_est.txt.gz 2016-07-17 11:27 3.5M
chr4_est.txt.gz 2016-07-17 11:27 3.7M
blastHg18KG.txt.gz 2010-05-11 17:01 3.7M
chr7_est.txt.gz 2016-07-17 11:27 4.0M
chr2_est.txt.gz 2016-07-17 11:28 4.1M
ensPep.txt.gz 2011-10-04 16:28 4.4M
chr1_est.txt.gz 2016-07-17 11:27 5.2M
gc5Base.txt.gz 2010-05-11 16:51 9.4M
nestedRepeats.txt.gz 2010-05-11 16:59 11M
simpleRepeat.txt.gz 2010-05-11 16:44 14M
netMonDom5.txt.gz 2010-05-11 17:01 16M
estOrientInfo.txt.gz 2016-07-17 11:27 16M
xenoRefFlat.txt.gz 2020-09-02 07:33 33M
xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M
xenoRefGene.txt.gz 2020-09-02 07:33 37M
chainMm9.txt.gz 2010-05-11 17:00 48M
all_est.txt.gz 2016-07-17 11:28 50M
netMm9.txt.gz 2010-05-11 16:46 51M
netHg19.txt.gz 2010-05-11 16:46 59M
netBosTau7.txt.gz 2012-06-18 00:04 69M
rmsk.txt.gz 2010-05-11 16:44 108M
chainHg19.txt.gz 2010-05-11 17:01 118M
chainMonDom5.txt.gz 2010-05-11 16:59 152M
xenoMrna.txt.gz 2020-09-02 07:33 336M
chainMm9Link.txt.gz 2010-05-11 16:52 419M
chainMonDom5Link.txt.gz 2010-05-11 16:56 510M
chainHg19Link.txt.gz 2010-05-11 16:48 654M
chainBosTau7.txt.gz 2012-06-17 22:45 786M
chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G