Schema for Clone Ends - Mapping of clone libraries end placements
  Database: hg38    Primary Table: cloneEndmultipleMaps    Row Count: 775,629   Data last updated: 2015-06-18
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 10001int(10) unsigned Start position in chromosome
chromEnd 38066int(10) unsigned End position in chromosome
name ABC9-43887500N20varchar(255) Name of item
score 500int(10) unsigned Optional score, nominal range 0-1000
strand -char(1) + or -
thickStart 10001int(10) unsigned Start of where display should be thick (start codon)
thickEnd 38066int(10) unsigned End of where display should be thick (stop codon)
reserved 0int(10) unsigned Used as itemRgb as of 2004-11-22
blockCount 2int(10) unsigned Number of blocks
blockSizes 531,170longblob Comma separated list of block sizes
chromStarts 0,27895longblob Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr11000138066ABC9-43887500N20500-100013806602531,1700,27895
585chr11047136306ABC8-43248200D14750+104713630602146,7050,25130
585chr11228248411WI2-813M19750-12282484110290,1850,35944
585chr11234050964WI2-2013N16750+123405096402578,5350,38089
585chr11234050965WI2-1989L12750+123405096502250,6300,37995
585chr11247851563ABC10-44142200C8750+124785156302618,6550,38430
585chr11296818666ABC12-47035800L3750-129681866602229,2630,5435
585chr11366253676ABC22-680P15750+13662536760262,6350,39379
585chr11800954110ABC9-41256800J23750+180095411002559,6610,35440
585chr11801054130ABC9-43845400P5750+180105413002716,7060,35414

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.