This directory contains a dump of the UCSC genome annotation database for the
    Feb. 2019 (Mmul_10/rheMac10) assembly of the rhesus genome
    (rheMac10, The Genome Institute at Washington University School of Medicine) .

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/215
    https://www.ncbi.nlm.nih.gov/genome/assembly/2345051
    https://www.ncbi.nlm.nih.gov/bioproject/476474

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=rheMac10
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.soe.ucsc.edu, then go to
the directory goldenPath/rheMac10/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/rheMac10/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/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 rheMac10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac10 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Rhesus sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

4. Any redistribution of the data should carry this notice.

-----------------------------------------------------------------------------
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 - all_est.sql 2019-09-03 15:27 2.1K all_est.txt.gz 2019-09-03 15:27 4.0M all_mrna.sql 2019-09-03 15:27 2.1K all_mrna.txt.gz 2019-09-03 15:27 16M augustusGene.sql 2019-09-03 15:27 1.9K augustusGene.txt.gz 2019-09-03 15:27 2.3M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 124 chainHg19.sql 2019-09-03 15:27 1.7K chainHg19.txt.gz 2019-09-03 15:27 19M chainHg19Link.sql 2019-09-03 15:27 1.5K chainHg19Link.txt.gz 2019-09-03 15:28 205M chainHg38.sql 2019-09-03 15:29 1.7K chainHg38.txt.gz 2019-09-03 15:29 21M chainHg38Link.sql 2019-09-03 15:29 1.5K chainHg38Link.txt.gz 2019-09-03 15:29 210M chainMm10.sql 2019-09-03 15:30 1.7K chainMm10.txt.gz 2019-09-03 15:30 67M chainMm10Link.sql 2019-09-03 15:30 1.5K chainMm10Link.txt.gz 2019-09-03 15:31 514M chainMm39.sql 2020-10-21 09:09 1.7K chainMm39.txt.gz 2020-10-21 09:09 64M chainMm39Link.sql 2020-10-21 09:12 1.6K chainMm39Link.txt.gz 2020-10-21 09:12 500M chainNeoSch1.sql 2020-07-12 01:20 1.7K chainNeoSch1.txt.gz 2020-07-12 01:20 206M chainNeoSch1Link.sql 2020-07-12 01:26 1.6K chainNeoSch1Link.txt.gz 2020-07-12 01:26 846M chromAlias.sql 2019-09-03 15:33 1.4K chromAlias.txt.gz 2019-09-03 15:33 28K chromInfo.sql 2019-09-03 15:33 1.4K chromInfo.txt.gz 2019-09-03 15:33 19K cpgIslandExt.sql 2019-09-03 15:33 1.7K cpgIslandExt.txt.gz 2019-09-03 15:33 634K cpgIslandExtUnmasked.sql 2019-09-03 15:33 1.7K cpgIslandExtUnmasked.txt.gz 2019-09-03 15:33 1.6M cytoBandIdeo.sql 2019-09-03 15:33 1.5K cytoBandIdeo.txt.gz 2019-09-03 15:33 18K ensGene.sql 2020-09-01 11:00 1.9K ensGene.txt.gz 2020-09-01 11:00 3.6M ensGtp.sql 2020-09-01 11:00 1.4K ensGtp.txt.gz 2020-09-01 11:00 667K ensPep.sql 2020-09-01 11:12 1.3K ensPep.txt.gz 2020-09-01 11:12 16M ensemblSource.sql 2020-09-01 11:12 1.4K ensemblSource.txt.gz 2020-09-01 11:12 197K ensemblToGeneName.sql 2020-09-01 11:00 1.4K ensemblToGeneName.txt.gz 2020-09-01 11:00 321K estOrientInfo.sql 2019-09-03 15:33 1.8K estOrientInfo.txt.gz 2019-09-03 15:33 937K extNcbiRefSeq.sql 2019-09-03 15:33 1.4K extNcbiRefSeq.txt.gz 2019-09-03 15:33 89 gap.sql 2019-09-03 15:33 1.6K gap.txt.gz 2019-09-03 15:33 4.1K gapOverlap.sql 2019-09-03 15:33 1.8K gapOverlap.txt.gz 2019-09-03 15:33 91 gbLoaded.sql 2019-09-03 15:33 1.6K gbLoaded.txt.gz 2019-09-03 15:33 944 gc5BaseBw.sql 2019-09-03 15:33 1.3K gc5BaseBw.txt.gz 2019-09-03 15:33 67 genscan.sql 2019-09-03 15:33 1.7K genscan.txt.gz 2019-09-03 15:33 2.9M gold.sql 2019-09-03 15:33 1.7K gold.txt.gz 2019-09-03 15:33 41K grp.sql 2019-09-03 15:33 1.3K grp.txt.gz 2019-09-03 15:33 213 hgFindSpec.sql 2021-03-26 09:06 1.8K hgFindSpec.txt.gz 2021-03-26 09:06 1.2K history.sql 2019-09-03 15:29 1.6K history.txt.gz 2019-09-03 15:29 941 intronEst.sql 2019-09-03 15:30 2.1K intronEst.txt.gz 2019-09-03 15:30 2.2M microsat.sql 2019-09-03 15:33 1.5K microsat.txt.gz 2019-09-03 15:33 352K mrnaOrientInfo.sql 2019-09-03 15:33 1.8K mrnaOrientInfo.txt.gz 2019-09-03 15:33 4.2M ncbiRefSeq.sql 2019-09-03 15:33 1.9K ncbiRefSeq.txt.gz 2019-09-03 15:33 4.1M ncbiRefSeqCds.sql 2019-09-03 15:33 1.3K ncbiRefSeqCds.txt.gz 2019-09-03 15:33 469K ncbiRefSeqCurated.sql 2019-09-03 15:33 2.0K ncbiRefSeqCurated.txt.gz 2019-09-03 15:33 550K ncbiRefSeqLink.sql 2019-09-03 15:27 2.0K ncbiRefSeqLink.txt.gz 2019-09-03 15:27 2.3M ncbiRefSeqOther.sql 2019-09-03 15:27 1.3K ncbiRefSeqOther.txt.gz 2019-09-03 15:27 76 ncbiRefSeqPepTable.sql 2019-09-03 15:34 1.4K ncbiRefSeqPepTable.txt.gz 2019-09-03 15:34 12M ncbiRefSeqPredicted.sql 2019-09-03 15:34 2.0K ncbiRefSeqPredicted.txt.gz 2019-09-03 15:34 3.8M ncbiRefSeqPsl.sql 2019-09-03 15:27 2.1K ncbiRefSeqPsl.txt.gz 2019-09-03 15:27 5.9M nestedRepeats.sql 2019-09-03 15:28 1.9K nestedRepeats.txt.gz 2019-09-03 15:28 18M netHg19.sql 2019-09-03 15:29 2.1K netHg19.txt.gz 2019-09-03 15:29 22M netHg38.sql 2019-09-03 15:33 2.1K netHg38.txt.gz 2019-09-03 15:33 22M netMm10.sql 2019-09-03 15:33 2.1K netMm10.txt.gz 2019-09-03 15:33 72M netMm39.sql 2020-10-21 09:16 2.1K netMm39.txt.gz 2020-10-21 09:16 72M netNeoSch1.sql 2020-07-12 01:29 2.1K netNeoSch1.txt.gz 2020-07-12 01:29 77M refFlat.sql 2019-09-03 15:33 1.7K refFlat.txt.gz 2019-09-03 15:33 503K refGene.sql 2019-09-03 15:33 1.9K refGene.txt.gz 2019-09-03 15:33 552K refSeqAli.sql 2019-09-03 15:33 2.1K refSeqAli.txt.gz 2019-09-03 15:33 563K rhesusSNVs.sql 2020-05-19 14:27 1.3K rhesusSNVs.txt.gz 2020-05-19 14:27 72 rmsk.sql 2019-09-03 15:33 1.9K rmsk.txt.gz 2019-09-03 15:33 141M seqNcbiRefSeq.sql 2019-09-03 15:34 1.5K seqNcbiRefSeq.txt.gz 2019-09-03 15:34 1.3M simpleRepeat.sql 2019-09-03 15:34 1.9K simpleRepeat.txt.gz 2019-09-03 15:34 26M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 6.6K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 3.8K tandemDups.sql 2019-09-03 15:34 1.8K tandemDups.txt.gz 2019-09-03 15:34 30M trackDb.sql 2021-03-26 09:06 2.1K trackDb.txt.gz 2021-03-26 09:06 41K ucscToINSDC.sql 2019-09-03 15:34 1.4K ucscToINSDC.txt.gz 2019-09-03 15:34 25K ucscToRefSeq.sql 2019-09-03 15:34 1.4K ucscToRefSeq.txt.gz 2019-09-03 15:34 25K windowmaskerSdust.sql 2019-09-03 15:34 1.5K windowmaskerSdust.txt.gz 2019-09-03 15:34 146M xenoRefFlat.sql 2019-09-03 15:35 1.7K xenoRefFlat.txt.gz 2019-09-03 15:35 14M xenoRefGene.sql 2019-09-03 15:35 1.9K xenoRefGene.txt.gz 2019-09-03 15:35 16M xenoRefSeqAli.sql 2019-09-03 15:35 2.1K xenoRefSeqAli.txt.gz 2019-09-03 15:35 22M