This directory contains a dump of the UCSC genome annotation database for the
Jan. 2020 (ASM985889v3/wuhCor1) assembly of the wuhan seafood market pneumonia virus genome
(wuhCor1, 2019-nCoV) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/n/a
https://www.ncbi.nlm.nih.gov/genome/assembly/15851418
https://www.ncbi.nlm.nih.gov/bioproject/485481
https://www.ncbi.nlm.nih.gov/biosample/n/a
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=wuhCor1
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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.soe.ucsc.edu, then go to
the directory goldenPath/wuhCor1/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.soe.ucsc.edu/goldenPath/wuhCor1/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 wuhCor1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql wuhCor1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gold.sql 2020-01-29 11:07 1.7K
gold.txt.gz 2020-01-29 11:07 60
gap.sql 2020-01-29 11:07 1.6K
gap.txt.gz 2020-01-29 11:07 28
cpgIslandExtUnmasked.sql 2020-01-29 11:34 1.7K
cpgIslandExtUnmasked.txt.gz 2020-01-29 11:34 97
chromAlias.sql 2020-01-29 11:54 1.4K
chromAlias.txt.gz 2020-01-29 11:54 79
ucscToINSDC.sql 2020-01-29 12:01 1.4K
ucscToINSDC.txt.gz 2020-01-29 12:01 67
ucscToRefSeq.sql 2020-01-29 12:01 1.5K
ucscToRefSeq.txt.gz 2020-01-29 12:01 63
simpleRepeat.sql 2020-01-29 12:05 1.9K
simpleRepeat.txt.gz 2020-01-29 12:05 86
cytoBandIdeo.sql 2020-01-29 13:00 1.5K
cytoBandIdeo.txt.gz 2020-01-29 13:00 63
gc5BaseBw.sql 2020-01-29 13:00 1.3K
gc5BaseBw.txt.gz 2020-01-29 13:00 66
windowmaskerSdust.sql 2020-01-29 13:21 1.5K
windowmaskerSdust.txt.gz 2020-01-29 13:21 345
cpgIslandExt.sql 2020-01-29 13:23 1.7K
cpgIslandExt.txt.gz 2020-01-29 13:23 89
genscan.sql 2020-01-29 13:25 1.7K
genscan.txt.gz 2020-01-29 13:25 118
genscanSubopt.sql 2020-01-29 13:25 1.6K
genscanSubopt.txt.gz 2020-01-29 13:25 140
augustusGene.sql 2020-01-29 13:32 2.0K
augustusGene.txt.gz 2020-01-29 13:32 164
ncbiGene.sql 2020-01-29 13:54 1.7K
ncbiGene.txt.gz 2020-01-29 13:54 238
chromInfo.sql 2020-01-29 16:02 1.4K
chromInfo.txt.gz 2020-01-29 16:02 72
history.sql 2020-01-30 11:00 1.6K
history.txt.gz 2020-01-30 11:00 421
strainPhastConsElements44way.sql 2020-03-17 16:52 1.6K
strainPhastConsElements44way.txt.gz 2020-03-17 16:52 5.0K
strainPhastCons44way.sql 2020-03-17 16:54 1.8K
strainPhastCons44way.txt.gz 2020-03-17 16:54 830
strainName44way.sql 2020-03-17 17:00 1.6K
strainName44way.txt.gz 2020-03-17 17:00 71
strainName44wayFrames.sql 2020-03-17 17:47 1.8K
strainName44wayFrames.txt.gz 2020-03-17 17:47 218
strainPhyloP44way.sql 2020-03-17 17:52 1.8K
strainPhyloP44way.txt.gz 2020-03-17 17:52 1.0K
crisprDet.sql 2020-03-27 07:50 2.1K
crisprDet.txt.gz 2020-03-27 07:50 243
grp.sql 2020-03-29 02:07 1.4K
grp.txt.gz 2020-03-29 02:07 246
seq.sql 2020-04-09 16:18 1.5K
seq.txt.gz 2020-04-09 16:18 3.1K
primers.sql 2020-04-14 04:40 2.1K
primers.txt.gz 2020-04-14 04:40 1.2K
rfam.sql 2020-04-27 15:01 1.5K
rfam.txt.gz 2020-04-27 15:01 139
strainName119way.sql 2020-04-30 21:38 1.6K
strainName119way.txt.gz 2020-04-30 21:38 73
strainPhastConsElements119way.sql 2020-04-30 21:42 1.6K
strainPhastConsElements119way.txt.gz 2020-04-30 21:42 12K
strainPhastCons119way.sql 2020-04-30 21:43 1.8K
strainPhastCons119way.txt.gz 2020-04-30 21:43 862
strainPhyloP119way.sql 2020-04-30 21:44 1.8K
strainPhyloP119way.txt.gz 2020-04-30 21:44 1.0K
strainName119wayFrames.sql 2020-04-30 21:46 1.8K
strainName119wayFrames.txt.gz 2020-04-30 21:46 219
mafSnpStrainName44way.sql 2020-05-02 10:13 1.6K
mafSnpStrainName44way.txt.gz 2020-05-02 10:13 858K
mafSnpStrainName119way.sql 2020-05-02 10:23 1.6K
mafSnpStrainName119way.txt.gz 2020-05-02 10:23 1.0M
rnaStructRangan.sql 2020-05-04 12:51 1.6K
rnaStructRangan.txt.gz 2020-05-04 12:51 3.8K
multiz7way.sql 2020-05-13 10:49 1.6K
multiz7way.txt.gz 2020-05-13 10:49 67
multiz7wayFrames.sql 2020-05-13 11:30 1.8K
multiz7wayFrames.txt.gz 2020-05-13 11:30 204
mafSnp7way.sql 2020-05-13 11:34 1.5K
mafSnp7way.txt.gz 2020-05-13 11:34 94K
microdel.sql 2020-05-20 06:54 1.6K
microdel.txt.gz 2020-05-20 06:54 1.0K
extFile.sql 2020-06-21 08:31 1.4K
extFile.txt.gz 2020-06-21 08:31 173
trackDb.sql 2024-02-12 16:48 2.1K
trackDb.txt.gz 2024-02-12 16:48 181K
hgFindSpec.sql 2024-02-12 16:48 1.8K
hgFindSpec.txt.gz 2024-02-12 16:48 614
tableDescriptions.sql 2024-11-16 02:04 1.4K
tableDescriptions.txt.gz 2024-11-16 02:04 4.7K
tableList.sql 2024-11-17 03:14 1.6K
tableList.txt.gz 2024-11-17 03:14 2.3K
bigFiles.sql 2024-11-17 03:14 1.4K
bigFiles.txt.gz 2024-11-17 03:14 69