Schema for Clone Ends - Mapping of clone libraries end placements
  Database: hg38    Primary Table: cloneEndbadEnds    Row Count: 82,411   Data last updated: 2015-08-20
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 12364int(10) unsigned range Start position in chromosome
chromEnd 282557int(10) unsigned range End position in chromosome
name ABC27-372I13varchar(255) values Name of item
score 0int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -
thickStart 12364int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 282557int(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 623,715longblob   Comma separated list of block sizes
chromStarts 0,269478longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
73chr112364282557ABC27-372I130+1236428255702623,7150,269478
73chr112477280623ABC14-50092500M100+1247728062302625,6710,267475
73chr112693201941ABC12-49243200C180+1269320194102539,7410,188507
73chr113401744942ABC12-46740000L60+1340174494202355,5640,730977
73chr113520286799COR2A-DD0002TVCNU_J80-1352028679902855,8380,272441
73chr113572289992COR2A-DD0002UZVNU_I170+1357228999202808,8230,275597
73chr114543285112ABC8-40908400B80+1454328511202682,7260,269843
73chr114635284178ABC23-1977M220-1463528417802452,3430,269200
73chr114722203013ABC12-46674300N100+1472220301302708,6860,187605
73chr116032284512ABC11-49394500L100-1603228451202480,6810,267799

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 mappings from the NCBI Clone DB database. Libraries with more than 30,000 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/Homo_sapiens/ *.GCF_000001405.26.106.*.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 30,000 clones are included in this track display.

Click through on displayed items to the Clone DB database information, including Clone DB distributor references.

clone information from NCBI Clone DB and UCSC mapping statistics library
name
total
clones
total end
sequences
NCBI mapped
ends
UCSC filtered
ends
UCSC
dropped
per-cent
dropped
ABC82,007,0473,888,4761,205,4661,192,78412,682% 1.05
WI21,122,5642,298,885589,547582,8436,704% 1.14
ABC121,120,9392,169,280778,216771,8276,3890.82
ABC71,116,9662,152,975650,329644,0716,2580.96
ABC91,065,5032,084,892757,644750,6486,9960.92
ABC101,062,0822,121,489788,344781,3317,0130.89
ABC141,042,9292,089,193846,055839,1266,9290.82
ABC131,009,6432,057,345811,829803,5898,2401.01
ABC11998,8801,966,644730,565724,8645,7010.78
ABC23942,1331,535,766437,098433,8963,2020.73
ABC16907,9481,534,288452,316449,1013,2150.71
ABC24835,6001,383,475399,056395,7763,2800.82
ABC27768,3361,229,804334,232331,8222,4100.72
ABC18743,6401,204,811325,150322,9042,2460.69
COR2A723,5691,441,881583,327578,5784,7490.81
ABC22519,274780,151189,988188,7431,2450.66
ABC21436,930680,160182,214180,9731,2410.68
RP11292,975394,81386,87585,9039721.12
COR02272,396546,984208,377206,7821,5950.77
CTD226,848403,68896,59494,9411,6531.71
CH17176,209325,659105,805105,0607450.70
ABC2049,13280,35024,72024,4742461.00
UCSC
dropped
152,979n/an/an/an/an/a
multiple
mappings
775,629n/an/an/an/an/a

Credits

Additional information about the clone, including how it can be obtained, may be found at the NCBI Clone Registry. To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page.