Clone Ends Track Settings

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

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*Source*	Bac libraries	Fosmid library	MICER	Placements

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	Source^↓1	Track Name^↓2
hide	Bac libraries	C57BL/6N mouse BAC clone set	Data format
hide	Bac libraries	B94_mq1 129S7/SvEv ES cell BAC library	Data format
hide	Bac libraries	C3H iBAC library	Data format
hide	Bac libraries	CHORI-29 NOD/LtJ BAC library	Data format
hide	Bac libraries	DIL (Diabetes and Inflammation Laboratory) NOD BAC library	Data format
hide	MICER	MICER 5'Hprt library	Data format
hide	MICER	MICER 3'Hprt library	Data format
hide	Bac libraries	Mus musculus molossinus male BAC library 1	Data format
hide	Bac libraries	RPCI-23 C57BL/6J female BAC library	Data format
hide	Bac libraries	RPCI-24 C57BL/6J male BAC library	Data format
hide	Fosmid library	WIBR-1 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: Mouse Dec. 2011 (GRCm38/mm10)

Description

This track shows the NCBI clone end predictions from the retired NCBI Clone DB database. Libraries with more than 20,000 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/Mus_musculus/ *.GCF_000001635.22.103.*.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 20,000 clones are included in this track display.

library name	total clones	total end sequences	NCBI mapped ends	UCSC filtered ends	UCSC dropped	percent dropped
B6Ng01	128,007	253,638	98,478	95,837	2,641	2.68
bMQ	129,826	244,222	75,671	72,540	3,131	4.14
C3H	86,696	169,665	43,690	42,378	1,312	3.00
CH29	93,023	340,272	52,320	50,621	1,699	3.25
DN	180,218	665,070	106,463	100,472	5,991	5.63
MHPN	118,658	208,707	61,942	58,582	3,360	5.42
MHPP	67,769	112,081	30,594	28,550	2,044	6.68
MSMg01	175,178	337,471	83,677	78,772	4,905	5.86
RP23	175,999	553,274	85,082	83,062	2,020	2.37
RP24	163,859	294,217	52,470	50,849	1,621	3.09
WI1	907,213	1,822,723	337,591	324,259	13,332	3.95

Credits

Additional information about the clone, including how it can be obtained, was available at the retired NCBI Clone Registry. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI's Genome Data Viewer (GDV) using the sequence data currently in Clone DB. Clone DB users should refer to MGI for their continuing research needs.

Please contact NCBI with any comments, concerns, or if you need help with the use of Clone DB data.