This directory contains a dump of the UCSC genome annotation database for the
Dec. 2013 (GRCh38/hg38) assembly of the human genome
(hg38, GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/51
http://www.ncbi.nlm.nih.gov/genome/assembly/883148
http://www.ncbi.nlm.nih.gov/bioproject/31257
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=hg38
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/hg38/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/hg38/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/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 hg38 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql hg38 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
affyGnf1h.sql 2015-05-11 01:50 2.1K
affyGnf1h.txt.gz 2015-05-11 01:50 596K
affyU95.sql 2015-05-11 01:50 2.1K
affyU95.txt.gz 2015-05-11 01:50 2.1M
affyU133.sql 2015-05-11 01:50 2.1K
affyU133.txt.gz 2015-05-11 01:50 4.0M
all_est.sql 2019-10-20 09:33 2.1K
all_est.txt.gz 2019-10-20 09:33 432M
all_mrna.sql 2020-08-17 18:38 2.1K
all_mrna.txt.gz 2020-08-17 18:38 167M
all_sts_primer.sql 2015-09-07 06:44 2.1K
all_sts_primer.txt.gz 2015-09-07 06:44 9.6M
all_sts_seq.sql 2015-09-07 06:44 2.1K
all_sts_seq.txt.gz 2015-09-07 06:44 4.0M
altLocations.sql 2022-11-03 14:54 1.5K
altLocations.txt.gz 2022-11-03 14:54 11K
altSeqLiftOverPsl.sql 2022-11-03 16:16 2.2K
altSeqLiftOverPsl.txt.gz 2022-11-03 16:16 570K
altSeqLiftOverPslP3.sql 2015-06-01 02:23 2.1K
altSeqLiftOverPslP3.txt.gz 2015-06-01 02:23 18K
altSeqLiftOverPslP6.sql 2016-03-13 03:31 2.1K
altSeqLiftOverPslP6.txt.gz 2016-03-13 03:31 26K
augustusGene.sql 2022-10-18 23:39 2.0K
augustusGene.txt.gz 2022-10-18 23:39 2.6M
bigFiles.sql 2024-12-29 03:33 1.4K
bigFiles.txt.gz 2024-12-29 03:33 2.2K
bioCycMapDesc.sql 2024-08-19 15:16 1.4K
bioCycMapDesc.txt.gz 2024-08-19 15:16 5.5K
bioCycPathway.sql 2024-08-19 15:16 1.5K
bioCycPathway.txt.gz 2024-08-19 15:16 22K
ccdsGene.sql 2019-10-20 09:43 1.9K
ccdsGene.txt.gz 2019-10-20 09:43 2.1M
ccdsInfo.sql 2019-10-20 09:35 1.4K
ccdsInfo.txt.gz 2019-10-20 09:35 1.3M
ccdsKgMap.sql 2021-01-26 13:10 1.5K
ccdsKgMap.txt.gz 2021-01-26 13:10 819K
ccdsNotes.sql 2019-10-20 09:35 1.4K
ccdsNotes.txt.gz 2019-10-20 09:35 20K
ceBlastTab.sql 2024-08-19 15:16 1.7K
ceBlastTab.txt.gz 2024-08-19 15:16 118K
centromeres.sql 2014-08-17 12:08 1.5K
centromeres.txt.gz 2014-08-17 12:08 1.5K
cgapAlias.sql 2021-01-26 16:50 1.4K
cgapAlias.txt.gz 2021-01-26 16:50 1.3M
cgapBiocDesc.sql 2021-01-26 16:50 1.4K
cgapBiocDesc.txt.gz 2021-01-26 16:50 6.8K
cgapBiocPathway.sql 2021-01-26 16:50 1.4K
cgapBiocPathway.txt.gz 2021-01-26 16:50 25K
chainAquChr2.sql 2019-02-17 03:24 1.7K
chainAquChr2.txt.gz 2019-02-17 03:24 17M
chainAquChr2Link.sql 2019-02-17 03:23 1.5K
chainAquChr2Link.txt.gz 2019-02-17 03:23 144M
chainBosTau9.sql 2019-06-09 03:29 1.7K
chainBosTau9.txt.gz 2019-06-09 03:29 158M
chainBosTau9Link.sql 2019-06-09 03:30 1.5K
chainBosTau9Link.txt.gz 2019-06-09 03:31 810M
chainCalJac4.sql 2020-09-03 23:43 1.7K
chainCalJac4.txt.gz 2020-09-03 23:43 545M
chainCalJac4Link.sql 2020-09-03 23:58 1.6K
chainCalJac4Link.txt.gz 2020-09-03 23:58 1.6G
chainCanFam4.sql 2020-04-03 00:54 1.7K
chainCanFam4.txt.gz 2020-04-03 00:54 402M
chainCanFam4Link.sql 2020-04-03 01:06 1.6K
chainCanFam4Link.txt.gz 2020-04-03 01:06 1.2G
chainCanFam6.sql 2021-05-17 21:54 1.7K
chainCanFam6.txt.gz 2021-05-17 21:54 217M
chainCanFam6Link.sql 2021-05-17 22:02 1.6K
chainCanFam6Link.txt.gz 2021-05-17 22:02 939M
chainChlSab2.sql 2016-10-30 08:17 1.7K
chainChlSab2.txt.gz 2016-10-30 08:17 18M
chainChlSab2Link.sql 2016-10-30 08:17 1.5K
chainChlSab2Link.txt.gz 2016-10-30 08:17 191M
chainCriGriChoV2.sql 2019-06-09 03:34 1.7K
chainCriGriChoV2.txt.gz 2019-06-09 03:34 459M
chainCriGriChoV2Link.sql 2019-06-09 03:35 1.6K
chainCriGriChoV2Link.txt.gz 2019-06-09 03:37 1.4G
chainDanRer11.sql 2017-11-05 08:01 1.7K
chainDanRer11.txt.gz 2017-11-05 08:01 235M
chainDanRer11Link.sql 2017-11-05 08:02 1.5K
chainDanRer11Link.txt.gz 2017-11-05 08:02 535M
chainDasNov3.sql 2018-01-07 08:24 1.7K
chainDasNov3.txt.gz 2018-01-07 08:24 422M
chainDasNov3Link.sql 2018-01-07 08:25 1.5K
chainDasNov3Link.txt.gz 2018-01-07 08:27 1.5G
chainEnhLutNer1.sql 2020-05-17 03:30 1.7K
chainEnhLutNer1.txt.gz 2020-05-17 03:30 221M
chainEnhLutNer1Link.sql 2020-05-17 03:31 1.6K
chainEnhLutNer1Link.txt.gz 2020-05-17 03:32 899M
chainEquCab3.sql 2019-07-28 05:18 1.7K
chainEquCab3.txt.gz 2019-07-28 05:18 178M
chainEquCab3Link.sql 2019-07-28 05:19 1.5K
chainEquCab3Link.txt.gz 2019-07-28 05:20 898M
chainFelCat9.sql 2019-05-05 03:29 1.7K
chainFelCat9.txt.gz 2019-05-05 03:30 352M
chainFelCat9Link.sql 2019-05-05 03:31 1.5K
chainFelCat9Link.txt.gz 2019-05-05 03:32 1.2G
chainGalGal6.sql 2018-11-11 06:55 1.7K
chainGalGal6.txt.gz 2018-11-11 06:55 19M
chainGalGal6Link.sql 2018-11-11 06:55 1.5K
chainGalGal6Link.txt.gz 2018-11-11 06:55 138M
chainGalVar1.sql 2016-09-18 09:28 1.7K
chainGalVar1.txt.gz 2016-09-18 09:28 652M
chainGalVar1Link.sql 2016-09-18 09:30 1.5K
chainGalVar1Link.txt.gz 2016-09-18 09:33 1.7G
chainGorGor6.sql 2019-11-21 09:03 1.7K
chainGorGor6.txt.gz 2019-11-21 09:03 50M
chainGorGor6Link.sql 2019-11-21 09:04 1.6K
chainGorGor6Link.txt.gz 2019-11-21 09:04 174M
chainHg19ReMap.sql 2020-02-11 12:16 1.7K
chainHg19ReMap.txt.gz 2020-02-11 12:16 134K
chainHg19ReMapAxtChain.sql 2020-02-11 12:19 1.8K
chainHg19ReMapAxtChain.txt.gz 2020-02-11 12:19 59K
chainHg19ReMapAxtChainLink.sql 2020-02-11 12:19 1.6K
chainHg19ReMapAxtChainLink.txt.gz 2020-02-11 12:19 1.0M
chainHg19ReMapLink.sql 2020-02-11 12:16 1.6K
chainHg19ReMapLink.txt.gz 2020-02-11 12:16 1.1M
chainHg38Patch11Link.sql 2017-09-10 17:56 1.6K
chainHg38Patch11Link.txt.gz 2017-09-10 17:56 1.3M
chainHprcGCA_018466835v1.sql 2023-10-14 13:54 1.8K
chainHprcGCA_018466835v1.txt.gz 2023-10-14 13:54 11K
chainHprcGCA_018466835v1Link.sql 2023-10-14 13:54 1.6K
chainHprcGCA_018466835v1Link.txt.gz 2023-10-14 13:54 9.5M
chainHprcGCA_018466845v1.sql 2023-10-14 13:54 1.8K
chainHprcGCA_018466845v1.txt.gz 2023-10-14 13:54 11K
chainHprcGCA_018466845v1Link.sql 2023-10-14 13:54 1.6K
chainHprcGCA_018466845v1Link.txt.gz 2023-10-14 13:54 9.3M
chainHprcGCA_018466855v1.sql 2023-10-14 13:54 1.8K
chainHprcGCA_018466855v1.txt.gz 2023-10-14 13:54 14K
chainHprcGCA_018466855v1Link.sql 2023-10-14 13:54 1.6K
chainHprcGCA_018466855v1Link.txt.gz 2023-10-14 13:54 9.5M
chainHprcGCA_018466985v1.sql 2023-10-14 13:54 1.8K
chainHprcGCA_018466985v1.txt.gz 2023-10-14 13:54 16K
chainHprcGCA_018466985v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018466985v1Link.txt.gz 2023-10-14 13:55 9.5M
chainHprcGCA_018467005v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018467005v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018467005v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018467005v1Link.txt.gz 2023-10-14 13:55 9.2M
chainHprcGCA_018467015v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018467015v1.txt.gz 2023-10-14 13:55 10K
chainHprcGCA_018467015v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018467015v1Link.txt.gz 2023-10-14 13:55 9.3M
chainHprcGCA_018467155v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018467155v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018467155v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018467155v1Link.txt.gz 2023-10-14 13:55 9.6M
chainHprcGCA_018467165v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018467165v1.txt.gz 2023-10-14 13:55 12K
chainHprcGCA_018467165v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018467165v1Link.txt.gz 2023-10-14 13:55 9.5M
chainHprcGCA_018469405v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469405v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018469405v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469405v1Link.txt.gz 2023-10-14 13:55 8.5M
chainHprcGCA_018469415v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469415v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018469415v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469415v1Link.txt.gz 2023-10-14 13:55 9.7M
chainHprcGCA_018469425v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469425v1.txt.gz 2023-10-14 13:55 16K
chainHprcGCA_018469425v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469425v1Link.txt.gz 2023-10-14 13:55 9.7M
chainHprcGCA_018469665v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469665v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018469665v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469665v1Link.txt.gz 2023-10-14 13:55 8.4M
chainHprcGCA_018469675v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469675v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018469675v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469675v1Link.txt.gz 2023-10-14 13:55 8.2M
chainHprcGCA_018469685v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469685v1.txt.gz 2023-10-14 13:55 11K
chainHprcGCA_018469685v1Link.sql 2023-10-14 13:55 1.6K
chainHprcGCA_018469685v1Link.txt.gz 2023-10-14 13:55 8.5M
chainHprcGCA_018469695v1.sql 2023-10-14 13:55 1.8K
chainHprcGCA_018469695v1.txt.gz 2023-10-14 13:55 13K
chainHprcGCA_018469695v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469695v1Link.txt.gz 2023-10-14 13:56 8.5M
chainHprcGCA_018469705v1.sql 2023-10-14 13:56 1.8K
chainHprcGCA_018469705v1.txt.gz 2023-10-14 13:56 11K
chainHprcGCA_018469705v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469705v1Link.txt.gz 2023-10-14 13:56 8.4M
chainHprcGCA_018469865v1.sql 2023-10-14 13:56 1.8K
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chainHprcGCA_018469865v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469865v1Link.txt.gz 2023-10-14 13:56 8.4M
chainHprcGCA_018469875v1.sql 2023-10-14 13:56 1.8K
chainHprcGCA_018469875v1.txt.gz 2023-10-14 13:56 9.6K
chainHprcGCA_018469875v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469875v1Link.txt.gz 2023-10-14 13:56 9.6M
chainHprcGCA_018469925v1.sql 2023-10-14 13:56 1.8K
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chainHprcGCA_018469925v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469925v1Link.txt.gz 2023-10-14 13:56 9.6M
chainHprcGCA_018469935v1.sql 2023-10-14 13:56 1.8K
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chainHprcGCA_018469935v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469935v1Link.txt.gz 2023-10-14 13:56 9.6M
chainHprcGCA_018469945v1.sql 2023-10-14 13:56 1.8K
chainHprcGCA_018469945v1.txt.gz 2023-10-14 13:56 16K
chainHprcGCA_018469945v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469945v1Link.txt.gz 2023-10-14 13:56 9.6M
chainHprcGCA_018469955v1.sql 2023-10-14 13:56 1.8K
chainHprcGCA_018469955v1.txt.gz 2023-10-14 13:56 17K
chainHprcGCA_018469955v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469955v1Link.txt.gz 2023-10-14 13:56 9.6M
chainHprcGCA_018469965v1.sql 2023-10-14 13:56 1.8K
chainHprcGCA_018469965v1.txt.gz 2023-10-14 13:56 13K
chainHprcGCA_018469965v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018469965v1Link.txt.gz 2023-10-14 13:56 8.2M
chainHprcGCA_018470425v1.sql 2023-10-14 13:56 1.8K
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chainHprcGCA_018470425v1Link.sql 2023-10-14 13:56 1.6K
chainHprcGCA_018470425v1Link.txt.gz 2023-10-14 13:56 9.2M
chainHprcGCA_018470435v1.sql 2023-10-14 13:56 1.8K
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chainHprcGCA_018470435v1Link.sql 2023-10-14 13:56 1.6K
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chainHprcGCA_018470445v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018470445v1Link.sql 2023-10-14 13:57 1.6K
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chainHprcGCA_018470455v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018470455v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018470455v1Link.txt.gz 2023-10-14 13:57 9.6M
chainHprcGCA_018470465v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018470465v1Link.sql 2023-10-14 13:57 1.6K
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chainHprcGCA_018471065v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471065v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471065v1Link.txt.gz 2023-10-14 13:57 8.6M
chainHprcGCA_018471075v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471075v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471075v1Link.txt.gz 2023-10-14 13:57 8.2M
chainHprcGCA_018471085v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471085v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471085v1Link.txt.gz 2023-10-14 13:57 8.7M
chainHprcGCA_018471095v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471095v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471095v1Link.txt.gz 2023-10-14 13:57 8.7M
chainHprcGCA_018471105v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471105v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471105v1Link.txt.gz 2023-10-14 13:57 8.5M
chainHprcGCA_018471345v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471345v1Link.sql 2023-10-14 13:57 1.6K
chainHprcGCA_018471345v1Link.txt.gz 2023-10-14 13:57 8.5M
chainHprcGCA_018471515v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471515v1Link.sql 2023-10-14 13:57 1.6K
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chainHprcGCA_018471525v1.sql 2023-10-14 13:57 1.8K
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chainHprcGCA_018471525v1Link.sql 2023-10-14 13:57 1.6K
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chainHprcGCA_018471535v1.sql 2023-10-14 13:57 1.8K
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iscaCuratedBenign.txt.gz 2021-10-11 04:34 1.9K
iscaCuratedPathogenic.sql 2021-10-11 04:34 1.8K
iscaCuratedPathogenic.txt.gz 2021-10-11 04:34 48K
iscaLikelyBenign.sql 2021-10-11 04:34 1.8K
iscaLikelyBenign.txt.gz 2021-10-11 04:34 377K
iscaLikelyPathogenic.sql 2021-10-11 04:34 1.8K
iscaLikelyPathogenic.txt.gz 2021-10-11 04:34 71K
iscaPathGainCum.sql 2021-10-11 04:38 1.5K
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iscaPathLossCum.txt.gz 2021-10-11 04:38 57K
iscaPathogenic.sql 2021-10-11 04:34 1.8K
iscaPathogenic.txt.gz 2021-10-11 04:34 657K
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lrg.txt.gz 2019-11-03 03:55 50
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wgEncodeRegDnaseUwHpfSignal.txt.gz 2015-06-22 02:07 100
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wgEncodeRegDnaseUwMonocytescd14ro01746Hotspot.txt.gz 2015-06-22 02:08 146
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wgEncodeRegDnaseUwMonocytescd14ro01746Signal.txt.gz 2015-06-22 02:08 134
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wgEncodeRegTxnCaltechRnaSeqGm12878R2x75Il200SigPooled.sql 2015-06-22 02:08 1.4K
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wgEncodeRegTxnCaltechRnaSeqHepg2R2x75Il200SigPooled.sql 2015-06-22 02:08 1.4K
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wgEncodeRegTxnCaltechRnaSeqNhlfR2x75Il200SigPooled.sql 2015-06-22 02:08 1.4K
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xenoEst.sql 2020-08-17 18:38 2.2K
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xenoMrna.sql 2020-08-17 18:38 2.1K
xenoMrna.txt.gz 2020-08-17 18:38 248M
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xenoRefFlat.txt.gz 2020-08-17 19:10 18M
xenoRefGene.sql 2020-08-17 19:10 2.0K
xenoRefGene.txt.gz 2020-08-17 19:10 20M
xenoRefSeqAli.sql 2020-08-17 19:17 2.1K
xenoRefSeqAli.txt.gz 2020-08-17 19:17 17M