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 -
mafSnpStrainName119way.txt.gz 2020-05-02 10:23 1.0M
mafSnpStrainName44way.txt.gz 2020-05-02 10:13 858K
trackDb.txt.gz 2024-02-12 16:48 181K
mafSnp7way.txt.gz 2020-05-13 11:34 94K
strainPhastConsElements119way.txt.gz 2020-04-30 21:42 12K
strainPhastConsElements44way.txt.gz 2020-03-17 16:52 5.0K
tableDescriptions.txt.gz 2024-11-16 02:04 4.7K
rnaStructRangan.txt.gz 2020-05-04 12:51 3.8K
seq.txt.gz 2020-04-09 16:18 3.1K
tableList.txt.gz 2024-11-17 03:13 2.3K
crisprDet.sql 2020-03-27 07:50 2.1K
primers.sql 2020-04-14 04:40 2.1K
trackDb.sql 2024-02-12 16:48 2.1K
augustusGene.sql 2020-01-29 13:32 2.0K
simpleRepeat.sql 2020-01-29 12:05 1.9K
strainPhastCons119way.sql 2020-04-30 21:43 1.8K
strainPhastCons44way.sql 2020-03-17 16:54 1.8K
strainPhyloP119way.sql 2020-04-30 21:44 1.8K
strainPhyloP44way.sql 2020-03-17 17:52 1.8K
strainName119wayFrames.sql 2020-04-30 21:46 1.8K
strainName44wayFrames.sql 2020-03-17 17:47 1.8K
multiz7wayFrames.sql 2020-05-13 11:30 1.8K
hgFindSpec.sql 2024-02-12 16:48 1.8K
cpgIslandExtUnmasked.sql 2020-01-29 11:34 1.7K
cpgIslandExt.sql 2020-01-29 13:23 1.7K
ncbiGene.sql 2020-01-29 13:54 1.7K
genscan.sql 2020-01-29 13:25 1.7K
gold.sql 2020-01-29 11:07 1.7K
gap.sql 2020-01-29 11:07 1.6K
strainPhastConsElements119way.sql 2020-04-30 21:42 1.6K
strainPhastConsElements44way.sql 2020-03-17 16:52 1.6K
history.sql 2020-01-30 11:00 1.6K
tableList.sql 2024-11-17 03:13 1.6K
genscanSubopt.sql 2020-01-29 13:25 1.6K
mafSnpStrainName119way.sql 2020-05-02 10:23 1.6K
mafSnpStrainName44way.sql 2020-05-02 10:13 1.6K
microdel.sql 2020-05-20 06:54 1.6K
strainName119way.sql 2020-04-30 21:38 1.6K
strainName44way.sql 2020-03-17 17:00 1.6K
rnaStructRangan.sql 2020-05-04 12:51 1.6K
multiz7way.sql 2020-05-13 10:49 1.6K
mafSnp7way.sql 2020-05-13 11:34 1.5K
cytoBandIdeo.sql 2020-01-29 13:00 1.5K
seq.sql 2020-04-09 16:18 1.5K
windowmaskerSdust.sql 2020-01-29 13:21 1.5K
rfam.sql 2020-04-27 15:01 1.5K
tableDescriptions.sql 2024-11-16 02:04 1.5K
ucscToRefSeq.sql 2020-01-29 12:01 1.5K
ucscToINSDC.sql 2020-01-29 12:01 1.4K
chromAlias.sql 2020-01-29 11:54 1.4K
extFile.sql 2020-06-21 08:31 1.4K
chromInfo.sql 2020-01-29 16:02 1.4K
bigFiles.sql 2024-11-17 03:13 1.4K
grp.sql 2020-03-29 02:07 1.4K
gc5BaseBw.sql 2020-01-29 13:00 1.3K
primers.txt.gz 2020-04-14 04:40 1.2K
microdel.txt.gz 2020-05-20 06:54 1.0K
strainPhyloP44way.txt.gz 2020-03-17 17:52 1.0K
strainPhyloP119way.txt.gz 2020-04-30 21:44 1.0K
strainPhastCons119way.txt.gz 2020-04-30 21:43 862
strainPhastCons44way.txt.gz 2020-03-17 16:54 830
hgFindSpec.txt.gz 2024-02-12 16:48 614
history.txt.gz 2020-01-30 11:00 421
windowmaskerSdust.txt.gz 2020-01-29 13:21 345
grp.txt.gz 2020-03-29 02:07 246
crisprDet.txt.gz 2020-03-27 07:50 243
ncbiGene.txt.gz 2020-01-29 13:54 238
strainName119wayFrames.txt.gz 2020-04-30 21:46 219
strainName44wayFrames.txt.gz 2020-03-17 17:47 218
multiz7wayFrames.txt.gz 2020-05-13 11:30 204
extFile.txt.gz 2020-06-21 08:31 173
augustusGene.txt.gz 2020-01-29 13:32 164
genscanSubopt.txt.gz 2020-01-29 13:25 140
rfam.txt.gz 2020-04-27 15:01 139
genscan.txt.gz 2020-01-29 13:25 118
cpgIslandExtUnmasked.txt.gz 2020-01-29 11:34 97
cpgIslandExt.txt.gz 2020-01-29 13:23 89
simpleRepeat.txt.gz 2020-01-29 12:05 86
chromAlias.txt.gz 2020-01-29 11:54 79
strainName119way.txt.gz 2020-04-30 21:38 73
chromInfo.txt.gz 2020-01-29 16:02 72
strainName44way.txt.gz 2020-03-17 17:00 71
bigFiles.txt.gz 2024-11-17 03:13 69
ucscToINSDC.txt.gz 2020-01-29 12:01 67
multiz7way.txt.gz 2020-05-13 10:49 67
gc5BaseBw.txt.gz 2020-01-29 13:00 66
ucscToRefSeq.txt.gz 2020-01-29 12:01 63
cytoBandIdeo.txt.gz 2020-01-29 13:00 63
gold.txt.gz 2020-01-29 11:07 60
gap.txt.gz 2020-01-29 11:07 28