Schema for STS Markers - STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
  Database: hg38    Primary Table: stsMap    Row Count: 303,436   Data last updated: 2015-08-22
Format description: STS marker and its position on golden path and various maps
fieldexampleSQL type info description
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 49785int(11) range Start position in chrom - negative 1 if unpositioned
chromEnd 49915int(10) unsigned range End position in chrom
name GDB:229298varchar(255) values Name of STS marker
score 500int(10) unsigned range Score of a marker = 1000 when placed uniquely, else 1500/(#placements) when placed in multiple locations
identNo 168197int(10) unsigned range Identification number of STS
ctgAcc AL627309.15varchar(255) values Contig accession number
otherAcc AC140725.3;AC008993.3varchar(255) values Accession number of other contigs that the marker hits
genethonChrom 0varchar(255) values Chromosome (no chr) from Genethon map or 0 if none
genethonPos 0float range Position on Genethon map
marshfieldChrom 0varchar(255) values Chromosome (no chr) from Marshfield map or 0 if none
marshfieldPos 0float range Position on Marshfield map
gm99Gb4Chrom 0varchar(255) values Chromosome (no chr) from GeneMap99 map or 0 if none
gm99Gb4Pos 0float range Position on gm99_bg4 map
shgcTngChrom 0varchar(255) values Chromosome (no chr) from shgc_tng map or 0 if none
shgcTngPos 0float range Position on shgc_tng map
shgcG3Chrom 0varchar(255) values Chromosome (no chr) from Stanford G3 map or 0 if none
shgcG3Pos 0float range Position on shgc_g3 map
wiYacChrom 0varchar(255) values Chromosome (no chr) from Whitehead YAC map or 0 if none
wiYacPos 0float range Position on wi_yac map
wiRhChrom 0varchar(255) values Chromosome (no chr) from Whitehead RH map or 0 if none
wiRhPos 0float range Position on wi_rh map
fishChrom 0varchar(255) values Chromosome (no chr) from FISH map or 0 if none
beginBand 0varchar(255) values Beginning of range of bands on FISH map
endBand 0varchar(255) values End of range of bands on FISH map
lab 0varchar(255) values Laboratory that placed the FISH clone
decodeChrom 0varchar(255) values Chromosome (no chr) from deCODE genetic map or 0 if none
decodePos 0float range Position on deCODE genetic map

Connected Tables and Joining Fields
        hg38.stsAlias.identNo (via stsMap.identNo)
      hg38.stsInfo2.identNo (via stsMap.identNo)
      hg38.fishClones.stsNames (via stsMap.name)
      hg38.stsAlias.trueName (via stsMap.name)
      hg38.stsInfo2.name (via stsMap.name)
      hg38.stsInfo2.otherNames (via stsMap.name)

Sample Rows
 
chromchromStartchromEndnamescoreidentNoctgAccotherAccgenethonChromgenethonPosmarshfieldChrommarshfieldPosgm99Gb4Chromgm99Gb4PosshgcTngChromshgcTngPosshgcG3ChromshgcG3PoswiYacChromwiYacPoswiRhChromwiRhPosfishChrombeginBandendBandlabdecodeChromdecodePos
chr14978549915GDB:229298500168197AL627309.15AC140725.3;AC008993.300000000000000000000
chr11851161852401293500134986FO538757.3AC215219.3;AC140725.300000000000000000000
chr1624048624306HUMC5269500101810AC114498.2AC131281.7;BX649379.1000000000000000000000
chr1629358629983PMC55343P1750215538AC114498.2J01415.200000000000000000000
chr1629650630626PMC113853P1750213925AC114498.2J01415.200000000000000000000
chr1631487632089PMC55343P2750215541AC114498.2J01415.200000000000000000000
chr1632295632843PMC20756P3750214801AC114498.2J01415.200000000000000000000
chr1632493632557D17S1653E500215891AC114498.2AC091154.3;J01415.200000000000000000000
chr1632528633108PMC55343P3750215542AC114498.2J01415.200000000000000000000
chr1632556632684RH98513750122803AC114498.2J01415.200000000000000000000

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

STS Markers (stsMap) Track Description
 

Description

This track shows locations of Sequence Tagged Site (STS) markers along the draft assembly. These markers have been mapped using either genetic mapping (Genethon, Marshfield, and deCODE maps), radiation hybridization mapping (Stanford, Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map) techniques. Since August 2001, this track no longer displays fluorescent in situ hybridization (FISH) clones, which are now displayed in a separate track.

Genetic map markers are shown in blue; radiation hybrid map markers are shown in black. When a marker maps to multiple positions in the genome, it is shown in a lighter color.

Methods

Positions of STS markers are determined using both full sequences and primer information. Full sequences are aligned using blat, while isPCR (Jim Kent) and ePCR are used to find locations using primer information. Both sets of placements are combined to give final positions. In nearly all cases, full sequence and primer-based locations are in agreement, but in cases of disagreement, full sequence positions are used. Sequence and primer information for the markers were obtained from the primary sites for each of the maps, and from NCBI UniSTS (now part of NCBI Probe).

Using the Filter

The track filter can be used to change the color or include/exclude a set of map data within the track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter:

  • In the pulldown menu, select the map whose data you would like to highlight or exclude in the display. By default, the "All Genetic" option is selected.
  • Choose the color or display characteristic that will be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display data from the map selected in the pulldown list. If "include" is selected, the browser will display only data from the selected map.

When you have finished configuring the filter, click the Submit button.

Credits

This track was designed and implemented by Terry Furey. Many thanks to the researchers who worked on these maps, and to Greg Schuler, Arek Kasprzyk, Wonhee Jang, and Sanja Rogic for helping process the data. Additional data on the individual maps can be found at the following links: