Schema for Fosmid End Pairs - Fosmid End Pairs
  Database: hg18    Primary Table: fosEndPairs    Row Count: 386,129   Data last updated: 2006-03-27
Format description: Positions of end pairs for fosmids
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(6) range Bin number for browser speedup
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 2138int(10) unsigned range Start position of fosmid in chromosome
chromEnd 38279int(10) unsigned range End position of fosmid in chromosome
name G248P81012G10varchar(255) values Name of fosmid
score 750int(10) unsigned range 1000 if uniquely aligned, else 1500/(# of alignments to assembly)
strand -char(1) values Value should be + or -
pslTable all_fosendsvarchar(255) values Table which contains corresponding PSL records for linked features
lfCount 2int(10) unsigned range Number of linked features in the series
lfStarts 2138,38051longblob   Comma separated list of start positions of each linked feature in genomic
lfSizes 198,228longblob   Comma separated list of sizes of each linked feature in genomic
lfNames G248P81012RG10,G248P81012FG10longblob   Comma separated list of names of linked features

Connected Tables and Joining Fields
        hg18.all_fosends.qName (via fosEndPairs.lfNames)

Sample Rows
 
binchromchromStartchromEndnamescorestrandpslTablelfCountlfStartslfSizeslfNames
585chr1213838279G248P81012G10750-all_fosends22138,38051198,228G248P81012RG10,G248P81012FG10
585chr11014151701G248P8237G101000-all_fosends210141,51042635,659G248P8237RG10,G248P8237FG10
585chr166929105835G248P86718G71000-all_fosends266929,104704614,1131G248P86718RG7,G248P86718FG7
73chr1104447141412G248P88665E71000-all_fosends2104447,140769639,643G248P88665RE7,G248P88665FE7
73chr1104472141413G248P88665D61000-all_fosends2104472,140763612,650G248P88665RD6,G248P88665FD6
73chr1116643151352G248P85883G71000-all_fosends2116643,150640710,712G248P85883RG7,G248P85883FG7
586chr1220309255424G248P89720G101000+all_fosends2220309,254590613,834G248P89720FG10,G248P89720RG10
587chr1320427361858G248P83808D4750-all_fosends2320427,361460164,398G248P83808RD4,G248P83808FD4
587chr1324065365644G248P82985E2500-all_fosends2324065,365391267,253G248P82985RE2,G248P82985FE2
587chr1324165365673G248P82980H5500-all_fosends2324165,364967223,706G248P82980RH5,G248P82980FH5

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

Fosmid End Pairs (fosEndPairs) Track Description
 

Description

A valid pair of fosmid end sequences must be at least 30 kb but no more than 50 kb away from each other. The orientation of the first fosmid end sequence must be "+" and the orientation of the second fosmid end sequence must be "-".

Note: For hg19 and hg18 assemblies, the Fosmid End Pairs track is a main track under the "Mapping and Sequencing" track category.

On the hg38 assembly, the FOSMID End Pairs track is a subtrack within the Clone Ends track under the "Mapping and Sequencing" track category. Under the list of subtracks on the Clone Ends Track Settings page, the FOSMID End Pairs track is now named "WIBR-2 Fosmid library." With the WIBR-2 Fosmid library track setting on full, individual clone end mapping items are listed in the browser; click into any item to see details from NCBI.

Methods

End sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikin. Trimmed fosmid end sequences were placed on the assembled sequence using Jim Kent's blat program.

Credits

Sequencing of the fosmid ends was done at the Eli & Edythe L. Broad Institute of MIT and Harvard University. Clones are available through the BACPAC Resources Center at Children's Hospital Oakland Research Institute (CHORI).