Clone Ends Track Settings
 
Mapping of clone libraries end placements   (All Mapping and Sequencing tracks)

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 Bac libraries  C57BL/6N mouse BAC clone set   Schema 
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 Bac libraries  B94_mq1 129S7/SvEv ES cell BAC library   Schema 
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 Bac libraries  C3H iBAC library   Schema 
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 Bac libraries  CHORI-29 NOD/LtJ BAC library   Schema 
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 Bac libraries  DIL (Diabetes and Inflammation Laboratory) NOD BAC library   Schema 
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 Bac libraries  Mus musculus molossinus male BAC library 1   Schema 
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 Bac libraries  RPCI-23 C57BL/6J female BAC library   Schema 
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 Bac libraries  RPCI-24 C57BL/6J male BAC library   Schema 
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 Fosmid library  WIBR-1 fosmid library   Schema 
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 MICER  MICER 5'Hprt library   Schema 
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 MICER  MICER 3'Hprt library   Schema 
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 Placements  Clone end placements dropped at UCSC, map distance 3X median library size   Schema 
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 Placements  Clone end placements overlap coverage on the forward strand   Schema 
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 Placements  Clone end placements overlap coverage on the reverse strand   Schema 
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 Placements  Clone end placements that map to multiple locations in the genome   Schema 
    

Description

This track shows the NCBI clone end predictions from the 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.

Click through on displayed items to the Clone DB database information, including Clone DB distributor references.

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, 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.