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Clone Ends Track Settings
 
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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 Bac libraries  C57BL/6N mouse BAC clone set   Data format 
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 Bac libraries  B94_mq1 129S7/SvEv ES cell BAC library   Data format 
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 Bac libraries  C3H iBAC library   Data format 
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 Bac libraries  CHORI-29 NOD/LtJ BAC library   Data format 
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 Bac libraries  DIL (Diabetes and Inflammation Laboratory) NOD BAC library   Data format 
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 MICER  MICER 5'Hprt library   Data format 
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 MICER  MICER 3'Hprt library   Data format 
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 Bac libraries  Mus musculus molossinus male BAC library 1   Data format 
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 Bac libraries  RPCI-23 C57BL/6J female BAC library   Data format 
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 Bac libraries  RPCI-24 C57BL/6J male BAC library   Data format 
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 Fosmid library  WIBR-1 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: 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
B6Ng01128,007253,63898,47895,8372,6412.68
bMQ129,826244,22275,67172,5403,1314.14
C3H86,696169,66543,69042,3781,3123.00
CH2993,023340,27252,32050,6211,6993.25
DN180,218665,070106,463100,4725,9915.63
MHPN118,658208,70761,94258,5823,3605.42
MHPP67,769112,08130,59428,5502,0446.68
MSMg01175,178337,47183,67778,7724,9055.86
RP23175,999553,27485,08283,0622,0202.37
RP24163,859294,21752,47050,8491,6213.09
WI1907,2131,822,723337,591324,25913,3323.95

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.