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