Schema for Fosmid End Pairs - Fosmid End Pairs
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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
field | example | SQL type | info | description |
bin | 585 | smallint(6) | range | Bin number for browser speedup |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
chromStart | 2138 | int(10) unsigned | range | Start position of fosmid in chromosome |
chromEnd | 38279 | int(10) unsigned | range | End position of fosmid in chromosome |
name | G248P81012G10 | varchar(255) | values | Name of fosmid |
score | 750 | int(10) unsigned | range | 1000 if uniquely aligned, else 1500/(# of alignments to assembly) |
strand | - | char(1) | values | Value should be + or - |
pslTable | all_fosends | varchar(255) | values | Table which contains corresponding PSL records for linked features |
lfCount | 2 | int(10) unsigned | range | Number of linked features in the series |
lfStarts | 2138,38051 | longblob | | Comma separated list of start positions of each linked feature in genomic |
lfSizes | 198,228 | longblob | | Comma separated list of sizes of each linked feature in genomic |
lfNames | G248P81012RG10,G248P81012FG10 | longblob | | Comma separated list of names of linked features |
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Connected Tables and Joining Fields
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand | pslTable | lfCount | lfStarts | lfSizes | lfNames |
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585 | chr1 | 2138 | 38279 | G248P81012G10 | 750 | - | all_fosends | 2 | 2138,38051 | 198,228 | G248P81012RG10,G248P81012FG10 |
585 | chr1 | 10141 | 51701 | G248P8237G10 | 1000 | - | all_fosends | 2 | 10141,51042 | 635,659 | G248P8237RG10,G248P8237FG10 |
585 | chr1 | 66929 | 105835 | G248P86718G7 | 1000 | - | all_fosends | 2 | 66929,104704 | 614,1131 | G248P86718RG7,G248P86718FG7 |
73 | chr1 | 104447 | 141412 | G248P88665E7 | 1000 | - | all_fosends | 2 | 104447,140769 | 639,643 | G248P88665RE7,G248P88665FE7 |
73 | chr1 | 104472 | 141413 | G248P88665D6 | 1000 | - | all_fosends | 2 | 104472,140763 | 612,650 | G248P88665RD6,G248P88665FD6 |
73 | chr1 | 116643 | 151352 | G248P85883G7 | 1000 | - | all_fosends | 2 | 116643,150640 | 710,712 | G248P85883RG7,G248P85883FG7 |
586 | chr1 | 220309 | 255424 | G248P89720G10 | 1000 | + | all_fosends | 2 | 220309,254590 | 613,834 | G248P89720FG10,G248P89720RG10 |
587 | chr1 | 320427 | 361858 | G248P83808D4 | 750 | - | all_fosends | 2 | 320427,361460 | 164,398 | G248P83808RD4,G248P83808FD4 |
587 | chr1 | 324065 | 365644 | G248P82985E2 | 500 | - | all_fosends | 2 | 324065,365391 | 267,253 | G248P82985RE2,G248P82985FE2 |
587 | chr1 | 324165 | 365673 | G248P82980H5 | 500 | - | all_fosends | 2 | 324165,364967 | 223,706 | G248P82980RH5,G248P82980FH5 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Fosmid End Pairs (fosEndPairs) Track Description
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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).
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