Schema for Clone Ends - Mapping of clone libraries end placements
  Database: hg38    Primary Table: cloneEndABC18    Row Count: 322,904   Data last updated: 2015-06-18
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 19979int(10) unsigned range Start position in chromosome
chromEnd 59741int(10) unsigned range End position in chromosome
name ABC18-1845A23varchar(255) values Name of item
score 500int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 19979int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 59741int(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 535,446longblob   Comma separated list of block sizes
chromStarts 0,39316longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr11997959741ABC18-1845A23500-199795974102535,4460,39316
585chr12005859680ABC18-1893C131000-200585968002319,3280,39294
585chr12006459674ABC18-1583D4500-200645967402442,2520,39358
585chr13063071538ABC18-1837O20500+306307153802207,4240,40484
585chr14619084569ABC18-2024H12500+461908456902561,1890,38190
585chr14619284568ABC18-2016D2500+461928456802593,2510,38125
585chr190647130836ABC18-2185B13750-9064713083602129,3060,39883
73chr1111441146978ABC18-2522D17300-11144114697802584,3490,35188
73chr1111448146978ABC18-2366M5375-11144814697802633,6460,34884
73chr1111892189805ABC18-2142D14750-11189218980502356,3290,77584

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.