Schema for BAC End Pairs - BAC End Pairs
  Database: hg19    Primary Table: bacEndPairs    Row Count: 208,922   Data last updated: 2009-05-20
Format description: Standard linked features series table
fieldexampleSQL type info description
bin 73smallint(6) range Bin number for browser speedup
chrom chr1varchar(21) values Reference sequence chromosome or scaffold
chromStart 16012int(10) unsigned range Start position of clone in chromosome
chromEnd 139795int(10) unsigned range End position of clone in chromosome
name CTD-3214E10varchar(100) values Name of clone
score 1000int(10) unsigned range 1000 if uniquely aligned, else 1500/(# of alignments to assembly)
strand -char(2) values Value should be + or -
pslTable all_bacendsvarchar(50) values Table which contains corresponding PSL records for linked features
lfCount 2int(10) unsigned range Number of linked features in the series
lfStarts 16012,139374longblob   Comma separated list of start positions of each linked feature in genomic
lfSizes 430,421longblob   Comma separated list of sizes of each linked feature in genomic
lfNames AQ805270,AQ889555longblob   Comma separated list of names of linked features

Connected Tables and Joining Fields
        hg19.all_bacends.qName (via bacEndPairs.lfNames)
      hg19.fishClones.beNames (via bacEndPairs.lfNames) (via

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

BAC End Pairs (bacEndPairs) Track Description


Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 25 - 350 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.

This track shows these mappings in cases where both ends could be mapped. 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.

A valid pair of BAC end sequences must be at least 25 kb but no more than 350 kb away from each other. The orientation of the first BAC end sequence must be "+" and the orientation of the second BAC end sequence must be "-".

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).


BAC end sequences are placed on the assembled sequence using Jim Kent's blat program.


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.

Some BAC library clones (RPCI-11, and others) can be ordered from BACPAC Genomics, RIKEN, or from Thermofisher and possibly other companies.