UCSC Track Database Definition

Track Database Definition

How to declare Dataset Display Settings in the Genome Browser

Hub contributors should use the Hub Track specific version of this document.

This document describes how to declare dataset display characteristics in the Genome Browser through trackDb settings. Introducing new datasets for display in the Browser requires declaring the location and format of the data and defining initial display characteristics. In many cases, you may need to choose how the displayed data (aka "track") may be selected and configured. These settings are declared in a simple text file format and stored in a database called the "track database", or trackDb for short.

The text file format for trackDb settings follow the simple "ra" rules which establish a "record" as a set of related settings in a "stanza" delimited by blank lines. The first line of each stanza typically establishes the "key". Each line in a stanza will contain a single word "setting" name and one or more words or numbers that follow are the setting's "value". All trackDb stanzas are keyed by "track" and most will have certain common settings followed by track specific settings. Here is an example:

        track myFirstTrack
        type bed 6
        shortLabel Example Data
        longLabel The data in this track is format "bed 6".

Every track should have these four settings. The key of this track (myFirstTrack) is the name of the dataset. If the data is loaded into a MySQL table then the track name is almost always the table name. If the data is in one of the remote indexed file types (e.g. bigWig, bam, etc.) then the name is typically the root file name. However, this is a key to the track so it must be unique within the Genome Browser. (Data hubs need only declare track names unique to their hub.) After the "track" key, the most important setting for defining a track is the "type". This tells the Browser which format the data is in, defines how to display it, and determines which options are available for fine control of that display.

The remainder of this document is divided into the following sections and should be used as a ready reference.

Common trackDb settings
Settings by track type – with examples
- bed/bigBed: Item or region tracks
- wig/bigWig/bedGraph: Signal graphing tracks
- genePred: Gene models and predictions
- bam: Compressed Sequence Alignment/Map tracks
- pgSnp: Personal Genome SNP tracks
- vcfTabix: Variant Call Format
- psl: Sequence alignments
- chain and netAlign: Paired sequence alignments
- wigMaf: Multiple alignments
- expRatio: Microarray expression data
- snp: Short genetic variants from dbSNP
- Specialize or rarely used:
  altGraphX, bedDetail, clonePos, ctgPos, downloadsOnly, encodeFiveC, factorSource, rmsk and snake.
Grouping tracks into sets and hierarchies – with examples
Special settings for custom tracks
Obscure or special cases – (aka Rejections)
Table of Contents

Open/close all details.

Common trackDb settings

Common Settings

`track`
`type`
`shortLabel`
`longLabel`
`visibility`
`html`

Common Optional Settings

`bigDataUrl <url/relativePath>`
`boxedCfg <on/off>`
`color <red,green,blue>`
`altColor <red,green,blue>`
`chromosomes <chr1,chr2,...>`
`configureByPopup <on/off>`
`dataVersion <str>`
Related settings: `directUrl <url>`
`hgsid on`
`iframeUrl <url>`
`iframeOptions <string>`
`otherDb <otherDb>`
`origAssembly <db>`
`pennantIcon <icon> [html [tip]]`
`priority <float>`
`release <alpha/beta/public>[,beta/public]`
`table <tableName>`
`tableBrowser <off/on> [table1 ...]`
`url <url>` `urlLabel <label>` `idInUrlSql <sql for id>`
`urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...`
`wgEncode on`

Settings by track type

Many settings are valid only for certain types of tracks. These track types are described below along with the settings specific to their types.

bed/bigBed - Item or region track settings

`type bed <3-12> [+/.]` `type bigBed <3-12> [+/.]`
`type bed5FloatScore` `type bedRnaElements` `type broadPeak` `type coloredExon` `type gvf` `type ld2` `type narrowPeak` `type peptideMapping`
`bigDataUrl <url/relativePath>`
`colorByStrand <red,green,blue> <red,green,blue>`
`compareGenomeLinks <db[.table[.column]]=label> [db[.table[.column] =label …]`
`denseCoverage <maxVal>`
`labelOnFeature <on/off>`
`exonArrows <on/off>`
`exonNumbers <on/off>`
`<column>Filter <low>[:<high>]` `scoreFilter <low>[:<high>]` `pValueFilter` `qValueFilter` `signalFilter` `<column>FilterLimits <low>[:<high>]` `<column>FilterByRange <off/on>`
`filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]`
`itemRgb on`
`maxItems <integer>`
`maxWindowToDraw <integer>`
`minGrayLevel <1-9>`
`noScoreFilter on`
`spectrum on` `scoreMax <integer>` `scoreMin <integer>`
`thickDrawItem <off/on>`

Less frequently used item track settings
`bedFilter on`
`bedNameLabel <label>`
Related settings: `baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >`
`baseColorUseCds <given/table <table>>`
`baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>`
`baseColorTickColor <lighterShade/contrastingColor>`
`showDiffBasesAllScales on`
`showDiffBasesMaxZoom <basesPerPixel>`
`showCdsAllScales`
`showCdsMaxZoom <basesPerPixel>`
`exonArrowsDense <off/on>`
`itemDetailsHtmlTable <table>`
`itemImagePath <path> <suffix>` `itemBigImagePath <path> <suffix>`
`linkIdInName on`
`mafTrack <trackName>`
`nextExonText <str>` `prevExonText <str>`
`showTopScorers #`
Examples of item base types

wig,bigWig - Signal graphing track settings

`type wig <low#> <high#>` `type bigWig <#> <#>`
`type bedGraph <field>` `minLimit <#>` `maxLimit<#>`
`alwaysZero <off/on>`
`autoScale <off/on>`
`bigDataUrl <url/relativePath>`
`graphTypeDefault points`
`maxHeightPixels <max:default:min>`
`maxWindowToQuery <integer>`
`negateValues <on>`
`spanList <s1>[,s2…]`
`smoothingWindow <off/1-16>`
`transformFunc <NONE/LOG>`
`viewLimits <lower:upper>` `viewLimitsMax <lower:upper>`
`wigColorBy <bedTable>`
`windowingFunction <mean/mean+whiskers/maximum/minimum>`
`yLineMark <#>` `yLineOnOff <off/on>` `gridDefault on`
Examples of signal graphing tracks

genePred - Gene model track settings

`type genePred [pepTable [mrnaTable]]`
Related settings: `geneClasses <cl1 cl2...>`
`gClass_<xxx> <red,green,blue>`
`itemClassTbl <table>`
`itemClassNameColumn <col>`
`itemClassClassColumn <col>`
`filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]`
`autoTranslate 0`
`intronGap <#bases>`
`defaultLinkedTables <table1>[,table2...]`
`idXref <idColumn> <altIdColumn>`
`oldToNew <tableName>`
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. baseColorUseSequence, baseColorDefault, itemDetailsHtmlTable, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Examples of genePred tracks

bam - Compressed Sequence Alignment track settings

`type bam`
`bigDataUrl <url/relativePath>`
Related settings: `bamColorMode <strand/gray/tag/off>`
`bamGrayMode <aliQual/baseQual/unpaired>` `aliQualRange <min:max>` `baseQualRange <min:max>`
`bamColorTag <XX>`
`noColorTag .`
`bamSkipPrintQualScore .`
`indelDoubleInsert <off/on>` `indelQueryInsert <off/on>` `indelPolyA <off/on>`
`minAliQual <#>`
Related settings: `pairEndsByName .`
`pairSearchRange <#>`
`showNames <on/off>`
Additional settings found in the "Item or region tracks" section are also available for displaying bam tags. baseColorUseSequence, baseColorDefault, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Example for bam track:

pgSnp - Personal Genome SNP track settings

`type pgSnp`
`pgPolyphenPredTab <arg>`
`pgSiftPredTab <arg>`
Example of a Personal Genome SNP track:

vcfTabix - Variant Call Format (indexed by tabix) track settings

`type vcfTabix`
`bigDataUrl <url/relativePath>`
Related settings: `hapClusterEnabled <true\|false>`
`hapClusterColorBy <altOnly\|refAlt\|base>`
`hapClusterTreeAngle <triangle\|rectangle>`
`hapClusterHeight <N>`
Related settings: `applyMinQual <true\|false>`
`minQual <Q>`
`minFreq <F>`
Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks. maxWindowToDraw
Example of a VCF track:

psl - Sequence alignment tracks settings

`type psl <subtype> [otherDb]`
`blastRef <assembly.table>`
`colorChromDefault off`
`pred <assembly.table>`
`pslSequence <no/all/different>`
`transMapGene <assembly.table>` `transMapInfo <table>` `transMapSrc <assembly.table>` `transMapTypeDesc <label>`
`ucscRetroInfo`
Additional settings defined elsewhere in this document are also available for displaying psl tracks. baseColorUseSequence, baseColorDefault, chainLinearGap, chainMinScore, indelDoubleInsert, indelQueryInsert, indelPolyA, itemDetailsHtmlTable, matrix, matrixHeader, maxItems, maxWindowToDraw, showCdsAllScales, showCdsMaxZoom, showDiffBasesAllScales, showDiffBasesMaxZoom, spectrum
Examples of psl alignment tracks

chain and netAlign - paired species alignment track settings

`type chain <otherDb>` `otherDb <otherDb>`
`type netAlign <otherDb> <otherChainTable>` `otherDb <otherDb>`
`chainColor <scheme>`
`chainLinearGap <loose/medium>`
`chainMinScore <#>`
`chainNormScoreAvailable <yes/no>`
`matrix <size> <#,#,#,#,…>` `matrixHeader <b1,b2,b3,b4>` `$matrix` token in html.
`spectrum on`
Examples of chain and netAlign tracks

wigMaf - Multiple alignment track settings

`type wigMaf <minVal> <maxVal>`
`frames <table>`
`irows off`
`itemFirstCharCase noChange`
`pairwiseHeight <#>`
`speciesCodonDefault <species>`
`speciesDefaultOff <species1> [species2 ...]`
Related settings: `speciesOrder <species1> [species2 …]`
`speciesGroups <sgroup1> [sgroup2 …]` `sGroup_<sgroupN> <species1> [species2 …]`
`summary <tableName>`
`treeImage <imageFile>`
`wiggle <table1> <leftLabel1> <uiLabel1> [table2 leftLabel2 uiLabelN ...]`
Examples of wigMaf tracks

expRatio - Microarray expression track settings

`type expRatio`
`expDrawExons on`
`expScale <#>`
`expStep <#>`
`expTable <tableName>`
`groupings <fileName>`
Example of an expRatio track:

snp - Short genetic variants from dbSNP track settings

`type bed 6 +`
`chimpDb <db>`
`chimpMacaqueOrthoTable <table>`
`chimpOrangMacOrthoTable <table>`
`codingAnnoLabel_<table> <text>`
`codingAnnotations <table>[,table]`
`defaultGeneTracks <genesTrack>[,genesTrack]`
`defaultMaxWeight <1\|2\|3>`
`hapmapPhase <II\|III>`
`macaqueDb <db>`
`orangDb <db>`
`snpExceptions <table>`
`snpExceptionDesc <table>`
`snpSeq <table>`
`snpSeqFile <path>`
Additional settings found in the "Item or region tracks" section are also available for displaying snp tracks. maxWindowToDraw
Example of a snp track:

Specialized or rarely used types:

NONE OF THESE ARE FOR HUBS. Nor are any of their settings.

altGraphX - Alternate splicing gene model track settings

`type altGraphX`
Example of an altGraphX track:

bedDetail - Text extended bed track settings

`type bedDetail <#>`
Additional settings defined elsewhere in this document are also available for displaying bedDetail tracks. itemRgb, url, urlLabel TODO: Currently almost no settings or configuration options are supported by bedDetail tracks. However, there is very little, in principle, that should prevent adding support for almost all the "Item or region tracks" settings.
Example of a bedDetail track:

clonePos - Genome coverage track settings

`type clonePos`
Example of a clonePos track:

ctgPos - Physical map contigs track settings

`type ctgPos`
Example of a ctgPos track:

downloadsOnly - Specialized downloadable file track settings

`type downloadsOnly`
`fileSortOrder ...`
Example of a Downloads Only track:

encodeFiveC - Five C Chromatin interaction track settings

`type encodeFiveC`
`interTable <tableName>`
`interTableKind <label>`
Example of an encodeFiveC track:

factorSource - Combined items track settings

`type factorSource`
`sourceTable <table>`
`inputTrackTable <table>`
`inputTableFieldDisplay <f1> [f2...]`
`filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]`
`motifTable <on>`
`motifTable <table>`
`motifPwmTable <table>`
`motifMapTable <table>`
`motifMaxWindow <window size>`
Example of a factorSource track:

rmsk - Repeat masking track settings

`type rmsk`
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. maxWindowToDraw, spectrum
Example of a Repeat Masking track:

snake - Self referencing alignment track settings

`type snake <db>` `otherDb <otherDb>`
Additional settings found in the "Item or region tracks" section are also available for displaying snake tracks. maxWindowToDraw, spectrum
Example of a snake track:

Grouping tracks into sets and hierarchies

All tracks have to be assigned to one predefined track group ("Mapping and sequencing", "Genes", etc).
In addition and depending on how closely related they are, tracks can be organized into one of three hierarchical containers:

"multiWig" container: when the tracks are all in signal (wiggle or bigWig) format and it makes sense to overlay them.
Example: a set of bigWig tracks with H3K27ac signal, all on the same scale
"composite" container: when the tracks are expected to be configured together or have an internal subgrouping, like cell type or cell treatment.
Example: a set of ChIP-bigBeds in three different cell types
"superTrack" container: when the tracks share no specific configuration and you mostly want to show them together.
Example: a set of composite tracks or a mix of bigBed, bigWig and bam

Predefined major track groupings setting

`group <groupId>`
Example of a track belonging to a predefined group:

Supertrack (Folders) track settings

`superTrack on`
`parent <superTrack>`
Example of a Supertrack:

Composite track settings

`compositeTrack on`
`parent <composite> [off/on]`
`allButtonPair on`
`centerLabelsDense <off/on>`
`dragAndDrop subTracks`
Example of a Composite track:

Composite track subgroup settings

`subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]` `subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]`
`subGroups <gTag1=mTag1?> [gTag2= mTag2?]`
`dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]`
`filterComposite <dim[A/B/C][=one]> [dimB dimC ...]`
`dimension<?>checked <mTag1a> [mTag1b …]`
`controlledVocabulary <pathToFile> <gTag#=mdbVar> [gTag#=mdbVar …]`
`sortOrder <gTag#=+/-> [gTag#=- …]`
`fileSortOrder <var=val> [var=val ...]`
Examples of Composite tracks with Subgroups

Composite track View settings

`subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]` `track <viewName>` `view <viewTag>`
`subGroups view=<vTag1>…` `parent <viewName> [off/on]`
`viewUi on`
`configurable <off/on>`
Example of a Composite track with Views:

Aggregate or Overlay track settings

`container multiWig`
`parent <containerTrack>`
`aggregate <transparentOverlay/stacked/solidOverlay/none>`
`showSubtrackColorOnUi on`
Example of an Aggregate track:

Special settings for custom tracks

Custom track specific settings

`genome`
`offset`
The following trackDb style settings are only set internally by the hgCustom CGI code.
`browserLines`
`dataUrl`
`dbTrackType`
`fieldCount`
`firstItemPos`
`htmlFile`
`htmlUrl`
`initialPos`
`inputType`
`itemCount`
`mafFile`
`maxChromName`
`origTrackLine`
`tdbType`
`wibFile`
`wigFile`

Obscure or special case settings. (aka Rejections)

Rejected "types":

axt – rare bed 3 variant (replaced with netAlign?), panTro1.axtNetHg16

drosophila/dp1/trackDb.ra:type axt dm1

human/hg13/trackDb.ra:type axt mm3

human/hg15/trackDb.ra:type axt mm3

worm/ce1/trackDb.ra:type axt cb1

worm/ce2/trackDb.ra:type axt cb1

bedLogR – encode 1% test only??? Not found with tdbQuery from *

human/encodeTest/wgEncodeMetaCheckTest.ra

chromGraph - ??? Not found in tdbQuery -strict from *

gff http://genome.ucsc.edu/FAQ/FAQformat.html#format3

Not found in tdbQuery -strict from *

gtf http://genome.ucsc.edu/FAQ/FAQformat.html#format4

Not found in tdbQuery -strict from *

maf – replaced by wigMaf hg17, tdbQuery -strict: 1 track: fr1.tbaFishBirdCFTR

http://genome.ucsc.edu/FAQ/FAQformat.html#format5

net but not netAlign - custom only??? Not found with tdbQuery non strict

sample – RARE bed variant, hg15.affyTranscriptome, Affymetrix Transcriptome

hg15.hg15Mm3L

Completely replaced by type wig and more recently bigWig

List of Miscellaneous Specal Case, Deprecated, Rejected or Rarely Used Settings

Rejected settings	For Types	Reason
`accession`	all ENCODE only	ENCODE only; DEPRCATED (replaced with mdb )
`canPack <off/on>`	all	NOT FOR HUBS. Deprecated. Almost tracks can be displayed in the five standard visibilities. However on some track types such as wiggles, `squish` and `pack` offer no real advantage over `dense` and `full`. By default, these tracks will not offer the less valuable visibilities. Nevertheless, you can make your track offer these visibilility choices by turning canPack on. Note: subtracks of composites will always offer all five choices. Example: canPack on
`cdsDrawDefault`	genePred	There are a number of occurrences of cdsDrawDefault in our trackDbs, always set to ‘genomic\ codons ‘. However, I have found no documentation and no code that references this setting.
`cdsDrawOptions`	psl	I have found no documentation and no code that references this setting. Also, I do not see it in our trackDbs.
`cdsEvidence`	genePred	Used by JK experimental tracks only as either `jkgTxCdsEvidence` or `jkgTxCdsEvidence2`. This will show an evidence table named in the setting.
`cell`	bed, bedGraph ENCODE only	Obsolete: replaced with metaDb.
`chip`	expRatio, bed ENCODE only	DROP (no takers in any of our trackDb.ra files)
`dateSubmitted`	bedGraph, bed ENCODE only	Obsolete: replaced with metaDb.
`dateUnrestricted`	bed ENCODE only	Obsolete: replaced with metaDb.
`db`	chain, netAlign, genePred, bed 3	Not found in any of our trackDb.ras. Further, this is the same as assembly so implicit.
`dbProfile`	all	In hg18 experimental and cancerGenomics only.
`dividers`	all	OBSOLETE: use sortOrder instead.
`endFudge`	bed	Special case for hg17 HGSV Discordant (variation) tracks. Used in hgc to fudge chromEnd, I think.
`ensArchive`	genePred	Only in danRer4 Ensembl NonCoding to generate an Ensembl URL.
`ensemblTranscriptIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`ensemblGeneIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`ensemblIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`expProbeTable`	expRatio	Can't find code that supports this.Rare: only in human. affyHumanExon "Affy All Exon"
`extTable`	all	This setting points to a one record table that holds the external filename. This should be replaced by: track, table or bigDataUrl. (rare bigWig hg18.brTestPlus experimental track)
`extraFields`	bed	OBSOLETE: replaced by looking up "as" table description. However, that method does not allow for: selective inclusion/exclusion of fields reordering fields formatting titles
`filePos`	all	Can't find this in any of our trackDb.ra files.
`filterTopScorers`	bed5FloatScoreWithFdr, bed5FloatScore ENCODE only	Currently only used by pilot encode 1%. Presents user option to limit to the top scoring N items. Might be useful in other MySQL table based tracks but how valuable is it?
`gainColor` `lossColor`	bed ENCODE only	Currently only used by pilot encode 1% in hg17.encodeDless. Provides special color for "gain" and "loss" items.
`graphType`	bedGraph	Not found in code. Probably typo of graphTypeDefault. (rare hg18.encodeRegulomeDnaseArray)
`hgGene`	genePred	Cannot find code for this. No effect. ???
`informant`	genePred	Special setting for N-SCAN genes. Swapped into html description page.
`inputTracksSubgroupDisplay`	bed, factorSource ENCODE only	Only in hg18/hg19 wgEncodeReg*Clustered tracks. In code #ifdef TO_BE_REMOVED.
`itemAttrTbl`	genePred	Only used in borEut13. transMapRefGene.
`linesAt`	chromGraph	Unused track type (tdbQuery -strict).
`longlabel`	genePred	Typo, should be longLabel.
`longLabelClip`	all	Only used in sacCer3 (tdbQuery -strict).
`mafDot`	wigMaf	Can't find this in any of our trackDb.ra files and only supported as cart var.
`mafDotDefault`	wigMaf	Can't find this in any of our trackDb.ra files.
`mapDispatcher`	expRatio	Only hg17 group "x" [tingwang 2007] and not in C.
`maxScore`	broadPeak	Obsolete, replaced with scoreFilterLimits.
`metadata`	all ENCODE only	OBSOLETE: replaced by metaDb. Currently only way for datHubs to have metadata dropdowns. Used by WashU hubs.
`mgiUrl`	bed	Special case variant of url used by no current tracks (tdbQuery -strict).
`mgiUrlLabel`	bed	Special case variant of url used by no current tracks (tdbQuery -strict).
`minMax`	chromGraph	Unused track type (tdbQuery -strict).
`minScore`	bed, narrowPeak, broadPeak	Obsolete, replaced with scoreFilterLimits.
`msaTable`	wig, wigMafProt, wigMaf	Only hiv tracks use this. Code in wigMaf display and is used to look up species order.
`ncbiAccXref`	bed	Special case used by hg17/hg18 kiddEichler tracks. Names a table to convert kiddEichler IDs to NCBI IDs and print links.
`nextItemButton`	all	This setting lets you override the Browser wide setting to disable nextItem arrows (which is off by default). When this is on, the nextItem arrows will show up for your track. The opposite does not seem to be the case, where nextItems are enabled, but you want to exclude them from your track.
`noInherit`	all	This one should be OBSOLETE but there continue to be edge cases where this setting has some affect. Currently only 2 places this is read this: in hdb to makesuperChildren inherit settings from their supertrack. This is done by putting the super settings into the child's settings hash. tdbQuery where it appears to have no affect.
`nonBedFieldsLabel`	bigBed	OBSOLETE when bigBed has "as" definitions. Instead, the extraFieldsPrint should pick up the non-standard bed fields straight from the as definition.
`notNCBI`	bed	Only used in drosophila dm2/dm3. Referenced in hgc.c code.
`ococci`	bed	Not referenced in any of our trackDb.ra files or in code.
`otherOrg`	chain, netAlign	Typo: should be otherDb.
`onlyVisibility`	all	Not universally supported (rightClick/subtrack cfg, etc.) so deprecate or else expand. This setting restricts the visibility options of a track to only one setting such as "`full`". (rare hg19.lincRNAsAllCellTypeTopView)
`otherDbTable`	bed	Special case for Jackson lab's QTL (Quantitative Trait Locus) tracks.
`pairedEndUrlFormat`	bed	Special case only used on kiddEichler track. This is another external URL variant.
`pairwise`	wigMaf	Deprecate, replaced by summary.
`patDb`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`patKey`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`patTable`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`pgDbLink`	bed	Special only used in hg18/hg19 Genome Variants so far. This setting is used to name one or more tables that hold links to phenotype and other databases for pgSnps. Each table must have chrom, chromStart, chromStop, name and srcUrl as fields. The links will be seen in the bed item details page and will be looked up in each listed table by item location. Example: pgDbLink pgKb1PhenCode pgKb1Snpedia pgKb1Hgmd
`private`	bed	Only used in human/hg7/trackDb.ra, and not even there using tdbQuery -strict. Prevents access to data by removing from trackList when doing "pruneEmpties". Gotta wonder when the track is ever seen in the browser or why it is a track at all.
`pslTable`	bed	Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same `illuminaProbesAlign` when track is "illuminaProbesAlign".) Used for making an hgcAnchor `htcIlluminaProbesAlign`.
`pubsArticleTable`	bed, psl	Special for publications track.
`pubsMarkerTable`	bed, psl	Special for publications track.
`pubsPslTrack`	bed, psl	Special for publications track.
`pubsSequenceTable`	bed, psl	Special for publications track.
`refSeqAnnoVersion`	genePred	Special for rheMac2.refSeqAnno track. Not found in code.
`scoreFilterMax`	bed, bedLogR, peptideMapping, bigBed	OBSOLETE: replaced by scoreFilterLimits
`searchMethod`	bed	Error. Should be part of searchTable stanza, not track stanza. TODO: Document searchTable stanza.
`searchType`	bed	Error. Should be part of searchTable stanza, not track stanza. TODO: Document searchTable stanza.
`selectSubject`	psl	Special only used in hiv(only used by hiv and h1n1. (Just h1n1 according to tdbQuery -strict).
`seqTable`	bed	Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same `illuminaProbesSeq` when track is "illuminaProbesAlign".) Used for making an hgcAnchor `htcIlluminaProbesAlign`.
`settingsByView`	all	OBSOLETE: replaced with "view in the middle" view as separate track.
`snpTable <table>`	bed gwasCatalog only	Special for gwasCatalog: table used to map dbSNP IDs to genomic coords
`snpVersion`	bed gwasCatalog only	Special for gwasCatalog: dbSNP build number of table used to map dbSNP IDs to genomic coords
`speciesTarget`	wigMaf	OBSOLETE. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with `#define BRANEY_SAYS_USETARG_IS_OBSOLETE.`
`speciesTree`	wigMaf	OBSOLETE. Replaced by treeImage. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with `#define BRANEY_SAYS_USETARG_IS_OBSOLETE.`
`speciesUseFile <fileName>`	wigMaf	Deprecated Much more rarely used, this setting can replace `speciesOrder` and `speciesGroups`. Set the `speciesUseFile` to a path relative to the apache cgi-bin. The file should contain a single species name as the first word of each line. Example: speciesUseFile speciesLists/conserved8Way.txt
`stripPrefix`	bam	Not yet implemented? Only on hg18.oneKGHighCovSeq experimental track.
`subgroups`	bed	Typo: should be subGroups.
`subTrack`	all	OBSOLETE: replaced with parent.
`symbolTable`	bed, genePred	In hgTracks, flyBaseGeneName() methods, if an item name is found in this symbol table, the symbol name will be shown instead. Found in drosophila and strangely rn4 RGD Genes (but table named in rn4 does not have a symbol column. Instead, symbol lookup is hard-coded to rgdGene2ToSymbol).
`txInfo`	genePred	Only seems to be used in experimental tracks in hg18 and mm8.
`urlName`	genePred	Not referenced in code and rarely used. (e.g. hg18: encodePseudogeneConsensus, encodePseudogeneYale).
`url2`	bed	Special cased second URL used much like url.
`url2Label`	bed	Special cased second URL label used much like urlLabel.
`useScore`	bed, factorSource, bed5FloatScore, broadPeak	Deprecate: replaced with spectrum as a slighly less obscurely named setting.
`vegaGeneIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`vegaTranscriptIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`visibilityViewDefaults`	all	OBSOLETE since view in the middle change. LOSE
`wgEncodeGencodeVersion`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeAttrs`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeExonSupport`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeGeneSource`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptSource`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePdb`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePubMed`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeRefSeq`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTag`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptSupport`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeUniProt`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePolyAFeature`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeAnnotationRemark`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptionSupportLevel`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`yLinOnOff`	wigMaf	Typo: should be yLineOnOff.
`yalePseudoAssoc`	all ENCODE Gencode Only	Special for ENCODE Gencode.
`yalePseudoUrl`	all ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`yaleUrl`	all ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.