Schema for Fosmid End Pairs - Fosmid End Pairs
  Database: hg19    Primary Table: fosEndPairs    Row Count: 384,442   Data last updated: 2010-12-28
Format description: Positions of end pairs for fosmids
fieldexampleSQL type info description
bin 585smallint(6) range Bin number for browser speedup
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 12275int(10) unsigned range Start position of fosmid in chromosome
chromEnd 48416int(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 12275,48188longblob   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
        hg19.all_fosends.qName (via fosEndPairs.lfNames)

Sample Rows
 
binchromchromStartchromEndnamescorestrandpslTablelfCountlfStartslfSizeslfNames
585chr11227548416G248P81012G10750-all_fosends212275,48188198,228G248P81012RG10,G248P81012FG10
585chr12027861838G248P8237G101000-all_fosends220278,61179635,659G248P8237RG10,G248P8237FG10
585chr177066115972G248P86718G71000-all_fosends277066,114841614,1131G248P86718RG7,G248P86718FG7
73chr1114584151549G248P88665E71000-all_fosends2114584,150906639,643G248P88665RE7,G248P88665FE7
73chr1114609151550G248P88665D61000-all_fosends2114609,150900612,650G248P88665RD6,G248P88665FD6
73chr1126780161489G248P85883G71000-all_fosends2126780,160777710,712G248P85883RG7,G248P85883FG7
73chr1230446265561G248P89720G101000+all_fosends2230446,264727613,834G248P89720FG10,G248P89720RG10
587chr1330564371995G248P83808D4750-all_fosends2330564,371597164,398G248P83808RD4,G248P83808FD4
587chr1334202375781G248P82985E2500-all_fosends2334202,375528267,253G248P82985RE2,G248P82985FE2
587chr1334302375810G248P82980H5500-all_fosends2334302,375104223,706G248P82980RH5,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).