Clone Ends Track Settings

Mapping of clone libraries end placements (All Mapping and Sequencing tracks)

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	Source^↓1	Track Name^↓2
Hide	Agencourt	Agencourt fosmid library 10	Data format
Hide	Agencourt	Agencourt fosmid library 11	Data format
Hide	Agencourt	Agencourt fosmid library 12	Data format
Hide	Agencourt	Agencourt fosmid library 13	Data format
Hide	Agencourt	Agencourt fosmid library 14	Data format
Hide	Agencourt	Agencourt fosmid library 16	Data format
Hide	Agencourt	Agencourt fosmid library 18	Data format
Hide	Agencourt	Agencourt fosmid library 20	Data format
Hide	Agencourt	Agencourt fosmid library 21	Data format
Hide	Agencourt	Agencourt fosmid library 22	Data format
Hide	Agencourt	Agencourt fosmid library 23	Data format
Hide	Agencourt	Agencourt fosmid library 24	Data format
Hide	Agencourt	Agencourt fosmid library 27	Data format
Hide	Agencourt	Agencourt fosmid library 7	Data format
Hide	Agencourt	Agencourt fosmid library 8	Data format
Hide	Agencourt	Agencourt fosmid library 9	Data format
Hide	Chori	CHORI BAC hydatidiform mole	Data format
Hide	Chori	BCGSC Human BAC Rearray (32k minimal tiling set, mostly RP11 and CTD)	Data format
Hide	Coriell	NHGRI-CORIELLE CORIELL-02-F-39-40KB	Data format
Hide	Coriell	NHGRI-CORIELLE CORIELL-02A-F-39-40KB	Data format
Hide	CalTech	CalTech BAC library D	Data format
Hide	RPCI	RPCI BAC library 11	Data format
Hide	WIBR	WIBR-2 Fosmid library	Data format
Hide	Placements	Clone end placements that map to multiple locations in the genome	Data format
Hide	Placements	Clone end placements dropped at UCSC, map distance 3X median library size	Data format
Hide Configure	Placements	Clone end placements overlap coverage on the forward strand	Data format
Hide 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. While the NCBI Clone DB database interface has been retired and is no longer available, they were archived and are still accessible for download at NCBI and through the UCSC Genome Browser.

Clone availability: most of the clone libraries shown here can no longer be ordered. Two librarires that we show are exceptions and are still available for ordering from BACPAC Genomics who still sells the libraries made by and formerly distributed by Children's Hospital Oakland Research Institute (CHORI): the BCGSC Human 32k BAC Re-Array (minimal tiling set, mostly RP11 and CTD clones) and the CHORI-17 (CH17) BAC library from a hydatidiform mole.

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
ABC8	2,007,047	3,888,476	1,205,466	1,192,784	12,682	% 1.05
WI2	1,122,564	2,298,885	589,547	582,843	6,704	% 1.14
ABC12	1,120,939	2,169,280	778,216	771,827	6,389	0.82
ABC7	1,116,966	2,152,975	650,329	644,071	6,258	0.96
ABC9	1,065,503	2,084,892	757,644	750,648	6,996	0.92
ABC10	1,062,082	2,121,489	788,344	781,331	7,013	0.89
ABC14	1,042,929	2,089,193	846,055	839,126	6,929	0.82
ABC13	1,009,643	2,057,345	811,829	803,589	8,240	1.01
ABC11	998,880	1,966,644	730,565	724,864	5,701	0.78
ABC23	942,133	1,535,766	437,098	433,896	3,202	0.73
ABC16	907,948	1,534,288	452,316	449,101	3,215	0.71
ABC24	835,600	1,383,475	399,056	395,776	3,280	0.82
ABC27	768,336	1,229,804	334,232	331,822	2,410	0.72
ABC18	743,640	1,204,811	325,150	322,904	2,246	0.69
COR2A	723,569	1,441,881	583,327	578,578	4,749	0.81
ABC22	519,274	780,151	189,988	188,743	1,245	0.66
ABC21	436,930	680,160	182,214	180,973	1,241	0.68
RP11	292,975	394,813	86,875	85,903	972	1.12
COR02	272,396	546,984	208,377	206,782	1,595	0.77
CTD	226,848	403,688	96,594	94,941	1,653	1.71
CH17	176,209	325,659	105,805	105,060	745	0.70
ABC20	49,132	80,350	24,720	24,474	246	1.00
UCSC dropped	152,979	n/a	n/a	n/a	n/a	n/a
multiple mappings	775,629	n/a	n/a	n/a	n/a	n/a

Credits

Many of the libraries shown here were constructed by Pieter J. de Jong and colleagues, including the RPCI-11 (RP11) library at the Roswell Park Cancer Institute, and the CHORI-17 (CH17) and BCGSC 32k Re-Array libraries at BACPAC Genomics (formerly at the Children's Hospital Oakland Research Institute, CHORI). For background on de Jong's role in building these clone libraries, see this Undark profile.

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.