This directory contains a dump of the UCSC genome annotation database for the
    Jun. 2020 (GRCm39/mm39) assembly of the mouse genome
    (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9)) 
from the Mouse Genome Sequencing Consortium.

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI 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:
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, then go to
the directory goldenPath/mm39/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:// .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -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 mm39 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql mm39 --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 - gap.sql 27-Jul-2020 13:01 1.6K gap.txt.gz 27-Jul-2020 13:01 4.0K gold.sql 27-Jul-2020 13:01 1.7K gold.txt.gz 27-Jul-2020 13:01 470K cpgIslandExtUnmasked.sql 27-Jul-2020 15:47 1.7K cpgIslandExtUnmasked.txt.gz 27-Jul-2020 15:47 527K chromAlias.sql 27-Jul-2020 15:48 1.4K chromAlias.txt.gz 27-Jul-2020 15:48 779 simpleRepeat.sql 27-Jul-2020 16:07 1.9K simpleRepeat.txt.gz 27-Jul-2020 16:07 38M microsat.sql 27-Jul-2020 16:07 1.5K microsat.txt.gz 27-Jul-2020 16:07 1.9M cytoBandIdeo.sql 27-Jul-2020 17:04 1.5K cytoBandIdeo.txt.gz 27-Jul-2020 17:04 743 gc5BaseBw.sql 27-Jul-2020 17:04 1.3K gc5BaseBw.txt.gz 27-Jul-2020 17:04 63 ucscToINSDC.sql 27-Jul-2020 17:04 1.4K ucscToINSDC.txt.gz 27-Jul-2020 17:04 688 grp.sql 27-Jul-2020 17:08 1.3K grp.txt.gz 27-Jul-2020 17:08 213 chromInfo.sql 27-Jul-2020 17:08 1.4K chromInfo.txt.gz 27-Jul-2020 17:08 583 windowmaskerSdust.sql 28-Jul-2020 09:18 1.5K windowmaskerSdust.txt.gz 28-Jul-2020 09:18 116M rmsk.sql 30-Jul-2020 08:37 1.9K rmsk.txt.gz 30-Jul-2020 08:37 135M nestedRepeats.sql 30-Jul-2020 08:39 1.9K nestedRepeats.txt.gz 30-Jul-2020 08:39 14M tandemDups.sql 30-Jul-2020 09:22 1.8K tandemDups.txt.gz 30-Jul-2020 09:22 18M cpgIslandExt.sql 30-Jul-2020 09:23 1.7K cpgIslandExt.txt.gz 30-Jul-2020 09:23 358K augustusGene.sql 30-Jul-2020 12:51 1.9K augustusGene.txt.gz 30-Jul-2020 12:51 2.3M genscan.sql 30-Jul-2020 18:23 1.7K genscan.txt.gz 30-Jul-2020 18:23 3.0M genscanSubopt.sql 30-Jul-2020 18:23 1.6K genscanSubopt.txt.gz 30-Jul-2020 18:23 6.2M crisprAllRanges.sql 13-Aug-2020 01:08 1.5K crisprAllRanges.txt.gz 13-Aug-2020 01:08 2.8K crisprAllTargets.sql 13-Aug-2020 01:39 1.3K crisprAllTargets.txt.gz 13-Aug-2020 01:39 66 all_mrna.sql 17-Aug-2020 17:04 2.1K all_mrna.txt.gz 17-Aug-2020 17:04 41M xenoMrna.sql 17-Aug-2020 17:05 2.1K xenoMrna.txt.gz 17-Aug-2020 17:05 193M refFlat.sql 17-Aug-2020 18:26 1.7K refFlat.txt.gz 17-Aug-2020 18:26 2.7M refGene.sql 17-Aug-2020 18:26 1.9K refGene.txt.gz 17-Aug-2020 18:26 3.0M xenoRefGene.sql 17-Aug-2020 18:26 1.9K xenoRefGene.txt.gz 17-Aug-2020 18:26 9.5M xenoRefFlat.sql 17-Aug-2020 18:26 1.7K xenoRefFlat.txt.gz 17-Aug-2020 18:26 8.5M refSeqAli.sql 17-Aug-2020 18:26 2.1K refSeqAli.txt.gz 17-Aug-2020 18:26 3.4M xenoRefSeqAli.sql 17-Aug-2020 18:26 2.1K xenoRefSeqAli.txt.gz 17-Aug-2020 18:26 17M estOrientInfo.sql 18-Aug-2020 00:14 1.8K estOrientInfo.txt.gz 18-Aug-2020 00:14 57M all_est.sql 18-Aug-2020 00:35 2.1K all_est.txt.gz 18-Aug-2020 00:35 213M mrnaOrientInfo.sql 18-Aug-2020 00:39 1.8K mrnaOrientInfo.txt.gz 18-Aug-2020 00:39 20M gbLoaded.sql 18-Aug-2020 00:53 1.6K gbLoaded.txt.gz 18-Aug-2020 00:53 1.5K chainHg38.sql 18-Aug-2020 09:26 1.7K chainHg38.txt.gz 18-Aug-2020 09:26 68M chainHg38Link.sql 18-Aug-2020 09:30 1.5K chainHg38Link.txt.gz 18-Aug-2020 09:30 541M netHg38.sql 18-Aug-2020 09:32 2.1K netHg38.txt.gz 18-Aug-2020 09:32 52M chainSynHg38.sql 18-Aug-2020 09:39 1.7K chainSynHg38.txt.gz 18-Aug-2020 09:39 380K chainSynHg38Link.sql 18-Aug-2020 09:41 1.5K chainSynHg38Link.txt.gz 18-Aug-2020 09:41 259M netSynHg38.sql 18-Aug-2020 09:41 2.1K netSynHg38.txt.gz 18-Aug-2020 09:41 47M chainRBestHg38.sql 18-Aug-2020 15:51 1.7K chainRBestHg38.txt.gz 18-Aug-2020 15:51 1.4M chainRBestHg38Link.sql 18-Aug-2020 15:53 1.6K chainRBestHg38Link.txt.gz 18-Aug-2020 15:53 262M netRBestHg38.sql 18-Aug-2020 15:55 2.1K netRBestHg38.txt.gz 18-Aug-2020 15:55 52M history.sql 08-Sep-2020 17:07 1.6K history.txt.gz 08-Sep-2020 17:07 818 tableDescriptions.sql 07-Oct-2020 02:04 1.4K tableDescriptions.txt.gz 07-Oct-2020 02:04 5.4K hgFindSpec.sql 08-Oct-2020 02:03 1.7K hgFindSpec.txt.gz 08-Oct-2020 02:03 665 trackDb.sql 08-Oct-2020 02:03 2.0K trackDb.txt.gz 08-Oct-2020 02:03 29K tableList.sql 29-Nov-2020 03:06 1.5K tableList.txt.gz 29-Nov-2020 03:06 2.8K bigFiles.sql 29-Nov-2020 03:06 1.3K bigFiles.txt.gz 29-Nov-2020 03:06 92