Schema for Clone Ends - Mapping of clone libraries end placements
  Database: mm10    Primary Table: cloneEndmultipleMaps    Row Count: 4,269   Data last updated: 2016-03-02
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 704smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 15644523int(10) unsigned range Start position in chromosome
chromEnd 15683005int(10) unsigned range End position in chromosome
name WI1-865B9varchar(255) values Name of item
score 750int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 15644523int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 15683005int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 2int(10) unsigned range Number of blocks
blockSizes 626,562longblob   Comma separated list of block sizes
chromStarts 0,37920longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
704chr11564452315683005WI1-865B9750-156445231568300502626,5620,37920
704chr11564452615682977WI1-865P15750+156445261568297702535,5760,37875
730chr11906505419104750WI1-1896B11750+190650541910475002553,2190,39477
97chr12550035625585925BMQ-278K12750-255003562558592502729,7770,84792
97chr12550043325585907BMQ-278L11750-255004332558590702683,7500,84724
818chr13057374930614154WI1-986K19750+305737493061415402729,6880,39717
869chr13726965137308483WI1-856P4750+372696513730848302164,4410,38391
869chr13726968837308482WI1-856B22750-372696883730848202362,5480,38246
1062chr16256347062604209WI1-1006C5750+625634706260420902240,2120,40527
1077chr16451070164552610WI1-1006A7750+645107016455261002589,1870,41722

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Clone Ends (cloneEndSuper) Track Description
 

Description

This track shows the NCBI clone end predictions from the retired NCBI Clone DB database. Libraries with more than 20,000 clones are included in this track display.

Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence.

These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments.

The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments).

Display Conventions and Configuration

Items in this track are colored according to their strand orientation. Blue indicates alignment to the forward strand, and green indicates alignment to the negative strand.

Methods

The mappings of these BAC end sequences are taken directly from the NCBI Clone DB FTP site ftp.ncbi.nih.gov/repository/clone/reports/Mus_musculus/ *.GCF_000001635.22.103.*.gff files.

UCSC filtered the NCBI Clone DB mapped ends to drop ends that mapped to a region that was three times longer than the median size of the clones in the library. Only libraries with more than 20,000 clones are included in this track display.

library
name		 total
clones		 total end
sequences		 NCBI mapped
ends		 UCSC filtered
ends		 UCSC
dropped		 percent
dropped
B6Ng01128,007253,63898,47895,8372,6412.68
bMQ129,826244,22275,67172,5403,1314.14
C3H86,696169,66543,69042,3781,3123.00
CH2993,023340,27252,32050,6211,6993.25
DN180,218665,070106,463100,4725,9915.63
MHPN118,658208,70761,94258,5823,3605.42
MHPP67,769112,08130,59428,5502,0446.68
MSMg01175,178337,47183,67778,7724,9055.86
RP23175,999553,27485,08283,0622,0202.37
RP24163,859294,21752,47050,8491,6213.09
WI1907,2131,822,723337,591324,25913,3323.95

Credits

Additional information about the clone, including how it can be obtained, was available at the retired NCBI Clone Registry. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI's Genome Data Viewer (GDV) using the sequence data currently in Clone DB. Clone DB users should refer to MGI for their continuing research needs.

Please contact NCBI with any comments, concerns, or if you need help with the use of Clone DB data.