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Set-Cookie: hguid=2417415217_O4O7u1j5l3JMAxOD3TTFG0dHQt1O; path=/; domain=.ucsc.edu; expires=Thu, 31-Dec-2037 23:59:59 GMT Content-Type:text/html Clone Ends Track Settings
Clone Ends Track Settings
 
Mapping of clone libraries end placements   (All Mapping and Sequencing tracks)

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  Source Agencourt  Chori  Coriell  CalTech  RPCI  WIBR  Placements 
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 Agencourt  Agencourt fosmid library 10   Data format 
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 Agencourt  Agencourt fosmid library 11   Data format 
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 Agencourt  Agencourt fosmid library 12   Data format 
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 Agencourt  Agencourt fosmid library 13   Data format 
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 Agencourt  Agencourt fosmid library 14   Data format 
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 Agencourt  Agencourt fosmid library 16   Data format 
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 Agencourt  Agencourt fosmid library 18   Data format 
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 Agencourt  Agencourt fosmid library 20   Data format 
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 Agencourt  Agencourt fosmid library 21   Data format 
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 Agencourt  Agencourt fosmid library 22   Data format 
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 Agencourt  Agencourt fosmid library 23   Data format 
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 Agencourt  Agencourt fosmid library 24   Data format 
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 Agencourt  Agencourt fosmid library 27   Data format 
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 Agencourt  Agencourt fosmid library 7   Data format 
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 Agencourt  Agencourt fosmid library 8   Data format 
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 Agencourt  Agencourt fosmid library 9   Data format 
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 Chori  CHORI BAC hydatidiform mole   Data format 
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 Coriell  NHGRI-CORIELLE CORIELL-02-F-39-40KB   Data format 
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 Coriell  NHGRI-CORIELLE CORIELL-02A-F-39-40KB   Data format 
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 CalTech  CalTech BAC library D   Data format 
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 RPCI  RPCI BAC library 11   Data format 
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 WIBR  WIBR-2 Fosmid library   Data format 
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 Placements  Clone end placements that map to multiple locations in the genome   Data format 
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 Placements  Clone end placements dropped at UCSC, map distance 3X median library size   Data format 
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 Configure 		 Placements  Clone end placements overlap coverage on the forward strand   Data format 
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 Configure 		 Placements  Clone end placements overlap coverage on the reverse strand   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

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.