Schema for fishClones
  Database: hg38    Primary Table: fishClones    Row Count: 9,731   Data last updated: 2015-07-31
Format description: Describes the positions of fishClones in the assembly
fieldexampleSQL type info description
chrom chr1varchar(25) values Reference sequence chromosome or scaffold
chromStart 56019int(10) unsigned range Start position in chromosome
chromEnd 56284int(10) unsigned range End position in chromosome
name CTD-2607H18varchar(25) values Name of clone
score 500int(10) unsigned range Score from 0-1000
placeCount 16int(10) unsigned range Number of FISH clone mappings. Some mappings may be from non-sequence based methods
bandStarts 5q35,8p23,7q32,6p25,4q26,7p...longblob   Starting band of FISH clone mapping
bandEnds 5q35,8p23,7q32,6p25,4q26,7p...longblob   Ending band of FISH clone mapping
labs FHCRC,FHCRC,FHCRC,FHCRC,FHC...longblob   Lab where clone FISH'd
placeType BAC Endvarchar(255) values How clone was placed on the sequence assembly
accCount 0int(10) unsigned range Number of accessions associated with the clone
accNames  longblob   Accession associated with clone
stsCount 0int(10) unsigned range Number of STS markers associated with this clone
stsNames  longblob   Names of STS markers
beCount 1int(10) unsigned range Number of BAC end sequences associated with this clone
beNames AQ544695longblob   Accessions of BAC ends

Connected Tables and Joining Fields
        hg38.gold.frag (via fishClones.accNames)
      hg38.seq.acc (via fishClones.accNames)
      hg38.cloneEndCTD.name (via fishClones.name)
      hg38.cloneEndRP11.name (via fishClones.name)
      hg38.stsAlias.trueName (via fishClones.stsNames)
      hg38.stsInfo2.name (via fishClones.stsNames)
      hg38.stsInfo2.otherNames (via fishClones.stsNames)
      hg38.stsMap.name (via fishClones.stsNames)

Sample Rows
 
chromchromStartchromEndnamescoreplaceCountbandStartsbandEndslabsplaceTypeaccCountaccNamesstsCountstsNamesbeCountbeNames
chr15601956284CTD-2607H18500165q35,8p23,7q32,6p25,4q26,7p22,1q44,1p36,2p25,7q11.1,1q42,7p11.1,15q26,19p13.3,16q24,2q135q35,8p23,7q32,6p25,4q26,7p22,1q44,1p36,2p25,7q11.1,1q42,7p11.1,15q26,19p13.3,16q24,2q14FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End001AQ544695
chr16892069415RP11-620F19300166q27,3q29,5q35,8p23,7q32,6p25,4q26,7p22,1q44,1p36,7q11.1,1q42,7p11.1,15q26,19p13.3,16q246q27,3q29,5q35,8p23,7q32,6p25,4q26,7p22,1q44,1p36,7q11.1,1q42,7p11.1,15q26,19p13.3,16q24FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End001AQ401675
chr19811498552CTD-2589I925031p36,9q34,8p231p36,9q34,8p23FHCRC,FHCRC,FHCRCBAC End001AQ472274
chr1348280471432CTD-2243O22500166p25,4q26,2q37,5p15.3,Yq11.2,7p22,1q44,1p36,1q42,17q25,15q26,19p13.3,16q24,2q13,13q34,16p13.36p25,4q26,2q37,5p15.3,Yq11.2,7p22,1q44,1p36,1q42,17q25,15q26,19p13.3,16q24,2q14,13q34,16p13.3FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End Pair002AQ087861,AQ146897
chr1348280471432CTD-2243O22750166p25,4q26,2q37,5p15.3,Yq11.2,7p22,1q44,1p36,1q42,17q25,15q26,19p13.3,16q24,2q13,13q34,16p13.36p25,4q26,2q37,5p15.3,Yq11.2,7p22,1q44,1p36,1q42,17q25,15q26,19p13.3,16q24,2q14,13q34,16p13.3FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End Pair002AQ087861,AQ146897
chr1453579454087CTD-2503F15214137p22,1p36,14q21,1q41,20p13,9q34,6q27,3q29,19p13.3,5q35,4q26,6p25,Yq11.27p22,1p36,14q21,1q41,20p13,9q34,6q27,3q29,19p13.3,5q35,4q26,6p25,Yq11.2FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End001AQ263369
chr1619820705981CTC-800G310001611p15,12p13,20p13,9q34,7q36,6q27,3q29,5q35,6p25,Yq11.2,7p22,1q44,1p36,15q26,19p13.3,16q2411p15,12p13,20p13,9q34,7q36,6q27,3q29,5q35,6p25,Yq11.2,7p22,1q44,1p36,15q26,19p13.3,16q24FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCAccession1AC127532.1502B73344,B73343
chr1619820705981CTC-800G310001611p15,12p13,20p13,9q34,7q36,6q27,3q29,5q35,6p25,Yq11.2,7p22,1q44,1p36,15q26,19p13.3,16q2411p15,12p13,20p13,9q34,7q36,6q27,3q29,5q35,6p25,Yq11.2,7p22,1q44,1p36,15q26,19p13.3,16q24FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCAccession1AC127532.1502B73344,B73343
chr1620145706409CTD-2189I537567p22,12q24.3,1p36,13q14,6q27,16q247p22,12q24.3,1p36,13q14,6q27,16q24FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End Pair002AQ216404,AQ221935
chr1620145706409CTD-2189I5100067p22,12q24.3,1p36,13q14,6q27,16q247p22,12q24.3,1p36,13q14,6q27,16q24FHCRC,FHCRC,FHCRC,FHCRC,FHCRC,FHCRCBAC End Pair002AQ216404,AQ221935

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

FISH Clones (fishClones) Track Description
 

Description

This track shows the location of fluorescent in situ hybridization (FISH)-mapped clones along the assembly sequence. The locations of these clones were obtained from the NCBI Human BAC Resource here. Earlier versions of this track obtained this information directly from the paper Cheung, et al. (2001).

More information about the BAC clones, including how they may be obtained, can be found at the Human BAC Resource and the Clone Registry web sites hosted by NCBI. To view Clone Registry information for a clone, click on the clone name at the top of the details page for that item.

Using the Filter

This track has a filter that can be used to change the color or include/exclude the display of a dataset from an individual lab. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. To use the filter:

  1. In the pulldown menu, select the lab whose data you would like to highlight or exclude in the display.
  2. 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 clones from the lab selected in the pulldown list. If "include" is selected, the browser will display clones only from the selected lab.

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

Credits

We would like to thank all of the labs that have contributed to this resource:

References

Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8. PMID: 11237021