| 
	      This section describes the format of each table in 
	      autoSql format.
 Affymetrix 10K SNP Detailstable affy10KDetails
"Information representing the Affymetrix 10K Mapping Array"
(       
    string     affyId;    "Affymetrix SNP id"
    string     rsId;      "RS identifier (some are null)"
    string     tscId;     "TSC identifier (some are null)"
    char[2]    baseA;     "The first allele (A)"
    char[2]    baseB;     "The second allele (B)"
    char[34]   sequenceA; "The A allele with flanking sequence"
    char[34]   sequenceB; "The B allele with flanking sequence"
    char[8]    enzyme;    "The enzyme that was used to prepare the sample (HindIII
			   or XbaI)"
)
Affymetrix 120K SNP Array Informationtable affyGenoDetails
"Information representing the Affymetrix 120K SNP array"
(       
    uint       affyId;    "Affymetrix SNP id"
    uint       rsId;      "RS identifier (some are null)"
    char[2]    baseA;     "The first allele (A)"
    char[2]    baseB;     "The second allele (B)"
    char[34]   sequenceA; "The A allele with flanking sequence"
    char[34]   sequenceB; "The B allele with flanking sequence"
    char[8]    enzyme;    "The enzyme that was used to prepare the sample (HindIII
			   or XbaI)"
    float      minFreq;   "The minimum allele frequency"
    float      hetzyg;    "The heterozygosity from all observations"
    float      avHetSE;   "The Standard Error for the average heterozygosity (not
			   used)"
    char[2]    NA04477;   "Individual 01"
    char[2]    NA04479;   "Individual 02"
    char[2]    NA04846;   "Individual 03"
    char[2]    NA11036;   "Individual 04"
    char[2]    NA11038;   "Individual 05"
    char[2]    NA13056;   "Individual 06"
    char[2]    NA17011;   "Individual 07"
    char[2]    NA17012;   "Individual 08"
    char[2]    NA17013;   "Individual 09"
    char[2]    NA17014;   "Individual 10"
    char[2]    NA17015;   "Individual 11"
    char[2]    NA17016;   "Individual 12"
    char[2]    NA17101;   "Individual 13"
    char[2]    NA17102;   "Individual 14"
    char[2]    NA17103;   "Individual 15"
    char[2]    NA17104;   "Individual 16"
    char[2]    NA17105;   "Individual 17"
    char[2]    NA17106;   "Individual 18"
    char[2]    NA17201;   "Individual 19"
    char[2]    NA17202;   "Individual 20"
    char[2]    NA17203;   "Individual 21"
    char[2]    NA17204;   "Individual 22"
    char[2]    NA17205;   "Individual 23"
    char[2]    NA17206;   "Individual 24"
    char[2]    NA17207;   "Individual 25"
    char[2]    NA17208;   "Individual 26"
    char[2]    NA17210;   "Individual 27"
    char[2]    NA17211;   "Individual 28"
    char[2]    NA17212;   "Individual 29"
    char[2]    NA17213;   "Individual 30"
    char[2]    PD01;      "Individual 31"
    char[2]    PD02;      "Individual 32"
    char[2]    PD03;      "Individual 33"
    char[2]    PD04;      "Individual 34"
    char[2]    PD05;      "Individual 35"
    char[2]    PD06;      "Individual 36"
    char[2]    PD07;      "Individual 37"
    char[2]    PD08;      "Individual 38"
    char[2]    PD09;      "Individual 39"
    char[2]    PD10;      "Individual 40"
    char[2]    PD11;      "Individual 41"
    char[2]    PD12;      "Individual 42"
    char[2]    PD13;      "Individual 43"
    char[2]    PD14;      "Individual 44"
    char[2]    PD15;      "Individual 45"
    char[2]    PD16;      "Individual 46"
    char[2]    PD17;      "Individual 47"
    char[2]    PD18;      "Individual 48"
    char[2]    PD19;      "Individual 49"
    char[2]    PD20;      "Individual 50"
    char[2]    PD21;      "Individual 51"
    char[2]    PD22;      "Individual 52"
    char[2]    PD23;      "Individual 53"
    char[2]    PD24;      "Individual 54"
)
Affymetrix Transcriptometable affyTranscriptome
"Describes (x,y) pairs of samples"
    ushort bin;                         "A field to speed indexing" 
    string  chrom;                      "Chromosome alignment is on"
    uint    chromStart;                 "Start position in chromosome"
    uint    chromEnd;                   "End position in chromosome"
    string  name;                       "Unique index given to each block of samples"
    uint    score;                      "Overall block score from 0 to 1000"
    char[1] strand;                     "Strand: + or -"
    uint    sampleCount;                "Number of samples in this block"
    uint[sampleCount] samplePosition;   "Base position of each sample in this
                                         block, relative to chromStart"
    uint[sampleCount] sampleHeight;     "Score for each sample (y-value) from 0 to
					 1000"
   )
Alternative Splicingtable altGraphX
"An alternatively-spliced gene graph"
    (
    string tName;                   	"Name of target sequence, often a chrom"
    int tStart;                     	"First bac touched by graph"
    int tEnd;                       	"Start position in first bac"
    string name;                    	"Human readable name"
    uint id;                        	"Unique ID"
    char[2] strand;                 	"+ or - strand"
    uint vertexCount;               	"Number of vertices in graph"
    ubyte[vertexCount] vTypes;      	"Type for each vertex"
    int[vertexCount] vPositions;    	"Position in target for each vertex"
    uint edgeCount;                 	"Number of edges in graph"
    int[edgeCount] edgeStarts;      	"Array with start vertex of edges"
    int[edgeCount] edgeEnds;        	"Array with end vertex of edges"
    table evidence[edgeCount] evidence; "Array of evidence tables containing references 
				  	 to mRNAs that support a particular edge"
    int[edgeCount] edgeTypes;       	"Type for each edge, ggExon, ggIntron, etc"
    int mrnaRefCount;               	"Number of supporting mRNAs"
    string[mrnaRefCount] mrnaRefs;  	"Ids of mrnas supporting this"
    int[mrnaRefCount] mrnaTissues;  	"Ids of tissues that mrnas come from, indexes 
					 into tissue table"
    int[mrnaRefCount] mrnaLibs;     	"Ids of libraries that mrnas come from, indexes 
					 into library table"
   )
Atlas Oncology Sitetable atlasOncoGene
"Table used to link into ATLAS Oncology site"
   (
   string locusSymbol;  "LocusLink Symbol"
   string atlasGene;    "ATLAS Gene"
   string otherGene;    "Other gene"
   string url;          "URL for corresonding ATLAS web page"
   )
 Bactig Positionstable bactigPos
"Bactig positions in chromosome coordinates (bed 4 +)."
    (
    string chrom;        "Chromosome"
    uint   chromStart;   "Start position in chromosome"
    uint   chromEnd;     "End position in chromosome"
    string name;         "Bactig"
    string startContig;  "First contig in this bactig"
    string endContig;    "Last contig in this bactig"
    )
BGI (Beijing Genomics Institute) SNPstable bgiSnp
"Beijing Genomics Institute SNP information as bed 4 +"
    (
    string chrom;       "Chromosome"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "BGI SNP name: snp.superctg.ctg.pos.type.strainID"
    char[1] snpType;    "S (substitution), I (insertion), or D (deletion)"
    uint readStart;     "Start position in alternate allele read"
    uint readEnd;       "End position in alternate allele read"
    uint qualChr;       "Quality score in reference assembly"
    uint qualReads;     "Quality score in alternate allele read"
    string snpSeq;      "'X->Y' or indel sequence"
    string readName;    "Name of alternate allele read"
    char[1] readDir;    "Direction of read relative to reference"
    char[4] inBroiler;  "SNP found in Broiler strain? yes, no or n/a if not covered"
    char[4] inLayer;    "SNP found in Layer strain? yes, no or n/a if not covered"
    char[4] inSilkie;   "SNP found in Silkie strain? yes, no or n/a if not covered"
    string primerL;     "Left primer sequence"
    string primerR;     "Right primer sequence"
    char[1] questionM;  "L for dubious indels, H for other indels and SNPs"
    string extra;       "Additional information"
    )
Bio Cyc Pathway Maptable bioCycMapDesc
"Decription of BioCyc pathway maps"
   (
   string mapID;        "BioCyc pathway map"
   string description;  "BioCyc pathway map description"
   )
 Bio Cyc Pathwaytable bioCycPathway
"BioCyc Pathway to Known Gene cross reference"
   (
   string kgID;         "Known Gene ID" 
   string geneID;       "Gene (RefSeq) ID"
   string mapID;        "BioCyc pathway map ID"
   )
 Blast OutputThe following definition is used for several tables that contain blast 
for various organisms.table blastTab
"Tab-delimited blast output file"
    (
    string query;	"Name of query sequence"
    string target;	"Name of target sequence"
    float identity;	"Percent identity"
    uint aliLength;	"Length of alignment"
    uint mismatch;	"Number of mismatches"
    uint gapOpen;	"Number of gap openings"
    uint qStart;	"Start in query (0 based)"
    uint qEnd;		"End in query (non-inclusive)"
    uint tStart;	"Start in target (0 based)"
    uint tEnd;		"End in target (non-inclusive)"
    double eValue;	"Expectation value"
    double bitScore;	"Bit score"
    )
Browser Extensible Data (BED)The following definition is used for several tables, which may use 4 or more of 
the fields.
 table bed
"Browser extensible data"
    (
    string chrom;      "Chromosome or FPC contig"
    uint   chromStart; "Start position in chromosome"
    uint   chromEnd;   "End position in chromosome"
    string name;       "Name of item"
    uint   score;      "Score from 0-1000"
    char[1] strand;    "+ or -"
    uint thickStart;   "Start of where display should be thick (start codon)"
    uint thickEnd;     "End of where display should be thick (stop codon)"
    uint reserved;     "Always zero for now"
    int blockCount;    "Number of blocks (a block contains no gaps)"
    int[blockCount] blockSizes; "Comma-separated list of block sizes"
    int[blockCount] blockStarts; "Start positions relative to chromStart."
    int expCount;      "Number of experiments."
    int[expCount] expIds; "Experiment IDs."
    int[expCount] expScores; "Experiment scores."
    )
Celera Coveragetable celeraCoverage
"Summary of large genomic Duplications from Celera Data"
    (
    string chrom;   	"Chromosome or FPC contig"
    uint chromStart;    "Start position in chromosome"
    uint chromEnd;      "End position in chromosome"
    string name; 	"Source of information"
    )
Celera Duplicationstable celeraDupPositive
"Summary of large genomic Duplications from Celera Data"
    (
    string chrom;   	"Chromosome or FPC contig"
    uint chromStart;    "Start position in chromosome"
    uint chromEnd;  	"End position in chromosome"
    string name;    	"Celera accession name"
    string fullname;    "Celera accession full name"
    float fracMatch;    "Fraction of matching bases"
    float bpalign;  	"Base pair alignment score"
    )
Celera Overlaytable celeraOverlay
"Celera assembly overlay in the public (NCBI) assembly"
    (
    string chrom;      	"Chromosome"
    uint chromStart;   	"Start position in chromosome"
    uint chromEnd;     	"End position in chromosome"
    string name;       	"Other chromosome and start"
    string otherChrom; 	"Other chromosome"
    uint otherStart;   	"Start in other chromosome"
    uint otherEnd;     	"End in other chromosome"
    char orient;       	"Strand/orientation (F or R)"
    char field1;       	"? (always M)"
    char field2;       	"? (r or u)"
    string localId;    	"?"
    string parentInfo; 	"?"
    string refId;      	"Reference ID"
    uint refStart;     	"Start position in reference"
    uint refLength;     "Length in reference"
    byte refOrient;   	"Strand/orientation in reference (-1 or 1)"
    string queryId;    	"Query ID"
    uint queryStart;    "Start position in query"
    uint queryLength;   "Length in query"
    byte queryOrient; 	"Strand/orientation in query (-1 or 1)"
    )
CGAP Aliastable cgapAlias
"Associates CGAP pathway IDs with gene symbols or mRNA accessions"
   (
   string cgapID;       "CGAP pathway ID"
   string alias;        "Gene symbol or mRNA"
   )
 CGAP/BioCarta Pathway Descriptionstable cgapBiocDesc
"CGAP/BioCarta pathway description"
  (
  string mapID;         "CGAP/BioCarta pathway map ID"
  string description;   "Description"
  )
 CGAP/BioCarta Pathway Cross-Referencetable cgapBiocPathway
"CGAP BioCarta pathway cross reference"
   (
   string cgapID;       "CGAP pathway ID"
   string mapID;        "BioCarta pathway ID"
   )
 Chain Alignmentstable chain
"Summary info about a chain of alignments"
   (
   double score; 	"Score of chain"
   string tName; 	"Target sequence name"
   uint tSize; 		"Target sequence size"
   uint tStart; 	"Alignment start position in target"
   uint tEnd; 		"Alignment end position in target"
   string qName; 	"Query sequence name"
   uint qSize; 		"Query sequence size"
   char qStrand; 	"Query strand"
   uint qStart; 	"Alignment start position in query"
   uint qEnd; 		"Alignment end position in query"
   uint id; 		"Chain ID"
   }
 Chain Linktable chainLink
"Alignment block in chain"
   (
   string tName; 	"Target sequence name"
   uint tStart; 	"Alignment start position in target"
   uint tEnd; 		"Alignment end position in target"
   uint qStart; 	"Start in query"
   uint chainId; 	"Chain ID in chain table"
   )
 Chimp/Human Simple Differencestable chimpSimpleDiff
"Simple differences between the chimp and human genome assemblies"
   (
   string chrom;        "Chromosome number"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string   tseq;	"Target sequence (A,T,C,G)"
   string   qseq;	"Query sequence (A,T,C,G)"
   )
 Chromosome Band Informationtable cytoBand
"Describes the positions of cytogenetic bands within a chromosome"
   (
   string chrom;        "Chromosome number"
   uint   chromStart;   "Start position in genoSeq"
   uint   chromEnd;     "End position in genoSeq"
   string name;         "Name of cytogenetic band"
   string gieStain;     "Giesma stain results"
   )
 Chromosome Informationtable chromInfo
"Chromosome names and sizes"
    (
    string chrom;       "Chromosome name"
    uint   size;        "Chromosome size"
    string fileName;    "Chromosome file (raw one byte per base)"
    )
Clone Fragment Positionstable chrN_gl
"Fragment positions in golden path"
    (
    ushort  bin;          "A field to speed indexing added to many 
                           tables August 2001"
    uint    matches;      "Number of bases that match that aren't repeats"
    uint    misMatches;   "Number of bases that don't match"
    string  frag;         "Fragment name"
    uint    start;        "Start position in golden path"
    uint    end;          "End position in golden path"
    char[1] strand;       "+ or - for strand"
    )
Clone Informationtable clonePos
"A clone's position and other info."
    (
    string  name;       "Name of clone including version"
    uint    seqSize;    "base count not including gaps"
    ubyte   phase;      "htg phase"
    string  chrom;      "Chromosome name"
    uint    chromStart; "Start in chromosome"
    uint    chromEnd;   "End in chromosome"
    char[1] stage;      "F/D/P for finished/draft/predraft"
    string  faFile;     "File with sequence."
    )
Contamination Informationtable contamination
"Contamination in assembly (bed 4 +)"
    (
    string chrom;      "Chromosome"
    uint   chromStart; "Start position in chromosome"
    uint   chromEnd;   "End position in chromosome"
    string name;       "Name (type of contamination: E.coli, vector etc)"
    string acc;        "NCBI accession where contamination was found"
    string ctg;        "Alternate name (e.g. WGS contig name)"
    int    len;        "Length of contaminated portion of sequence"
    )
Contig/Accession Maptable contigAcc
"Maps a contig to its accession."
    (
    string contig;      "Contig name"
    string acc;         "GenBank accession"
    )
Contig Informationtable ctgPos
"Where a contig is inside of a chromosome."
    (
    string contig;      "Name of contig"
    uint   size;        "Size of contig"
    string chrom;       "Chromosome name"
    uint   chromStart;  "Start in chromosome"
    uint   chromEnd;    "End in chromosome"
    )
Contig Information (Expanded)table ctgPos2
"Where a contig is inside of a chromosome including contig type information."
    (
    string contig;      "Name of contig"
    uint   size;        "Size of contig"
    string chrom;       "Chromosome name"
    uint   chromStart;  "Start in chromosome"
    uint   chromEnd;    "End in chromosome"
    char[1] type;       "(W)GS contig, (F)inished, (P)redraft, (D)raft, (O)ther"
    )
CpG Islandstable cpgIsland
"Describes CpG Islands of 50 bases or more that are at least 50% G/C"
   (
   string chrom;        "Chromosome or FPC contig"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string name;         "CpG Island"
   uint   minLength;    "Minimum Island Length"
   uint   cpgNum;       "Number of CpGs in island"
   uint   gcNum;        "Number of C and G in island"
   uint   perCpg;       "Percentage of island that is CpG"
   uint   perGc;        "Percentage of island that is C or G"
   )
 CpG Islands (Extended)table cpgIslandExt
"Describes the CpG Islands (includes observed/expected ratio)"
   (
   string chrom;        "Chromosome or FPC contig"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string name;         "CpG Island"
   uint   length;       "Island Length"
   uint   cpgNum;       "Number of CpGs in island"
   uint   gcNum;        "Number of C and G in island"
   uint   perCpg;       "Percentage of island that is CpG"
   uint   perGc;        "Percentage of island that is C or G"
   float  obsExp;	"Ratio of observed(cpgNum) to expected(numC*numG/length) 
			 CpG in island"
   )
 dbSnpRStable dbSnpRS 
"Information from dbSNP at the reference SNP level"
    (
    uint    rsId;    	"RS identifier"
    float   avHet;   	"Average heterozygosity from all observations"
    float   avHetSE; 	"Standard Error for the average heterozygosity from all 
			 observations"
    string  valid;   	"Validation status of the SNP"
    char[1] base1;   	"Base of the first allele"
    char[1] base2;   	"Base of the second allele"
    string  assembly; 	"Sequence in the ucsc assembly"
    string  alternate; 	"Sequence of the alternate allele"
    )
DNA Motiftable dnaMotif
"A gapless DNA motif"
    (
    string name;                        "Motif name"
    int columnCount;                    "Count of columns in motif"
    float[columnCount] aProb;           "Probability of A's in each column"
    float[columnCount] cProb;           "Probability of C's in each column"
    float[columnCount] gProb;           "Probability of G's in each column"
    float[columnCount] tProb;           "Probability of T's in each column"
    )
DupSpMrnatable dupSpMrna
"Duplicate mRNA/Protein entries that have identical CDS structures"
   (
   string mrnaID;        "mRNA ID name"
   string proteinID;     "Protein ID from UniProtKB"
   string dupMrnaID;     "mRNA ID of duplicated entry"
   string dupProteinId;  "Protein ID of duplicated entry"
   )
 EncodeRegionInfotable encodeRegionInfo
"Descriptive, assembly-independent information about ENCODE regions"
    (
    string name;        "Name of region"
    string descr;       "Description (gene region, random pick, etc.)"
    )
Ensembl Gene XReftable ensGtp
"Associates Ensembl gene, transcript, and protein IDs"
   (
   string gene; 	"Gene ID"
   string transcript; 	"Transcript ID"
   string protein; 	"Protein ID"
   )
 EnsemblXreftable ensemblXref
"Cross-reference info between transcript entries and translation entries of Ensembl 
genes"  
   (
   string db;			"Ensembl Database"
   int gene_id;			"Gene ID number"
   string gene_name;		"Gene name in database"
   int transcript_id;		"Transcript ID number"
   string transcript_name;	"Transcript name in database"
   uint translation_id;		"Translation ID number"
   string translation_name; 	"Translation name in database"
   string external_db;		"External database"
   string external_name;	"External status"
   )
 EnsemblXref2table ensemblXref2
"Cross-reference info between transcript entries and translation entries of Ensembl 
genes (alternative table used in some assemblies)"  
   (
   string transcript_name; 	"Transcript name"
   string translation_name; 	"Translation name"
   )
 EnsemblXref3table ensemblXref3
"A cross-reference table for Ensembl Genes."
   (
   string gene;            "Ensembl gene ID"
   string geneVer;         "Ensembl gene ID version number"
   string transcript;      "Ensembl transcript ID"
   string transcriptVer;   "Ensembl transcript ID version number"
   string protein;         "Ensembl protein ID"
   string proteinVer;      "Ensembl protein version number"
   string tremblAcc;       "UniProtKB  protein accession number"
   string swissDisplayId;  "UniProtKB protein display ID"
   string swissAcc;        "UniProtKB protein accession number"
   )
 Ensembl gene_xref TableEnsemble gene_xref table downloaded directly from the Ensembl ftp site (18.34 
release 11/04). Refer to the Ensembl site for details.  CAUTION: Ensembl sometimes
changes its table definitions and some fields may not contain the data that the 
name indicates, e.g. translation_name.
 table ensGeneXref
"Table gene_xref downloaded from Ensembl"
   (
   string db;                   "#"
   string analysis;             "#"
   string type;                 "#"
   int gene_id;                 "#"
   string gene_name;            "#"
   int[5] gene_version;         "#"
   int transcript_id;           "#"
   string transcript_name;      "#"
   int[5] transcript_version;   "#"
   int[5] translation_name;     "#"
   int translation_id;          "#"
   int[5] translation_version;  "#"
   string external_db;          "#"
   string external_name;        "#"
   char[10] external_status;    "#"
   )
 Ensembl transcript TableEnsembl transcript table downloaded directly from the Ensembl ftp site (18.34 
release 11/04). Refer to the Ensembl site for details.  CAUTION: Ensembl 
sometimes changes its table definitions and some fields may not contain the data 
that the name indicates.table ensTranscript
"Table transcript downloaded from Ensembl"
   (
   int id;                      "#"
   string db;                   "#"
   string analysis;             "#"
   string type;                 "#"
   int transcript_id;           "#"
   string transcript_name;      "#"
   int transcript_version;      "#"
   string chr_name;             "#"
   int chr_start;               "#"
   int chr_end;                 "#"
   int chr_strand;              "#"
   int coding_start;            "#"
   int coding_end;              "#"
   int translation_id;          "#"
   string translation_name;     "#"
   string translation_version;  "#"
   int gene_id;                 "#"
   string gene_name;            "#"
   int gene_version;            "#"
   lstring exon_structure;      "#"
   lstring exon_ids;            "#"
   string external_db;          "#"
   string external_name;        "#"
   char[10] external_status;    "#"
   )
 Exofish Informationtable exoFish
"An evolutionarily conserved region (ecore) with Tetroadon"
   (
   string chrom;        "Chromosome or FPC contig"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string name;         "Just a dummy dot"
   uint   score;        "Score from 0 to 1000"
   )
 Exonerate Mouse HomologiesLast used Apr. 2001.table exoMouse
"A rough alignment - not detailed"
   (
   string chrom;        "Chromosome or FPC contig"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string name;         "Name of other sequence"
   uint   score;        "Score from 0 to 1000"
   char[1] strand;      " or -"
   uint otherStart;     "Start in other sequence"
   uint otherEnd;       "End in other sequence"
   )
 Experiment Recordtable expRecord
"Minimal descriptive data for an experiment in the browser"
   (
   uint id; 			"Internal id of experiment"
   string name; 		"Name of experiment"
   lstring description; 	"Description of experiment"
   lstring url; 		"URL relevant to experiment"
   lstring ref; 		"Reference for experiment"
   lstring credit; 		"Who to credit with experiment"
   uint numExtras; 		"Number of extra things"
   lstring[numExtras] extras; 	"Extra things of interest, i.e. classifications"
   )
 Expression Datatable expData
"Expression data (no mapping, just spots)"
   (
   string name; 		"Name of gene/target/probe etc."
   uint expCount; 		"Number of scores"
   float[expCount] expScores; 	"Scores. May be absolute or relative ratio"
   )
 Expression Distance Between 2 Genes
 table expDistance
"Distance between two genes in expression space"
    (
    string query;       "Name of one gene"
    string target;      "Name of other gene"
    float distance;     "Distance in expression space, always >= 0"
    )
FISH Clonestable fishClones
"Describes the positions of fishClones in the assembly"
   (
   string chrom;                   "Chromosome number"
   uint   chromStart;              "Start position in chromosome"
   uint   chromEnd;                "End position in chromosome"
   string name;                    "Name of clone"
   uint score;                     "Always 1000"
   uint placeCount;                "Number of times FISH'd"
   string[placeCount] bandStarts;  "Start FISH band"
   string[placeCount] bandEnds;    "End FISH band"
   string[placeCount] labs;        "Lab where clone FISH'd"
   string placeType;               "How clone was placed on the sequence assembly"
   uint accCount;                  "Number of accessions associated with the clone"
   string[accCount] accNames;      "Accession associated with clone"
   uint stsCount;                  "Number of STS markers associated with this clone"
   string[stsCount] stsNames;      "Names of STS  markers"
   uint beCount;                   "Number of BAC end sequences associated with this 
				    clone"
   string[beCount] beNames;        "Accessions of BAC ends"
   )
 FlyBase Accessions Linked to UniProtKB Accessionstable flyBaseSwissProt
"FlyBase acc to UniProtKB acc, plus some other UniProtKB info"
    (
    string flyBaseId;	"FlyBase FBgn ID"
    string swissProtId;	"UniProtKB ID"
    string spGeneName;	"Gene name from UniProtKB (long)"
    string spSymbol;	"Symbolic-looking gene ID from UniProtKB"
    )
FlyBase Allelestable fbAllele
"The alleles of a gene"
    (
    int id;		"Allele ID"
    string geneId;	"FlyBase ID of gene"
    string name;	"Allele name"
    )
FlyBase Gene Synonymstable fbSynonym
"Links all the names we call a gene to its FlyBase ID"
    (
    string geneId;	"FlyBase ID"
    string name;	"A name (synonym or real)"
    )
FlyBase Genestable fbGene
"Links FlyBase IDs, gene symbols and gene names"
    (
    string geneId;	"FlyBase ID"
    string geneSym;	"Short gene symbol"
    string geneName;	"Gene name - up to a couple of words"
    )
FlyBase Genes Cross-Reference (2004)table flyBase2004Xref
"FlyBase cross references circa late 2004 (dm2/4.0; dp3/1.0 uses a subset)"
    (
    string name;                "FlyBase annotation gene ID"
    string symbol;              "Symbolic gene name"
    lstring synonyms;           "Comma-separated list of synonyms"
    string fbtr;                "FlyBase FBtr acc"
    string fbgn;                "FlyBase FBgn acc"
    string fbpp;                "FlyBase FBpp acc"
    string fban;                "FlyBase FBan acc"
    string type;                "Annotation type (for noncoding only)"
    )
FlyBase Genes Linked to BDGP Transcript IDstable fbTranscript
"Links FlyBase gene IDs and BDGP transcript IDs"
    (
    string geneId;	 "FlyBase gene ID"
    string transcriptId; "BDGP Transcript ID"
    )
FlyBase Genes Linked to GO IDstable fbGo
"Links FlyBase gene IDs and GO IDs/aspects"
    (
    string geneId;      "FlyBase gene ID"
    string goId;        "GO ID"
    string aspect;      "P (process), F (function) or C (cellular component)"
    )
FlyBase Observed Phenotype in Mutanttable fbPhenotype
"Observed phenotype in mutant. Sometimes contains gene function info"
    (
    string geneId;	"FlyBase gene ID"
    int fbAllele;	"ID in fbAllele table or 0 if not allele-specific"
    int fbRef;		"ID in fbRef table"
    lstring text;	"Descriptive text"
    )
FlyBase Referencetable fbRef
"A literature or sometimes database reference"
    (
    int id;		"Reference ID"
    lstring text;	"Usually begins with FlyBase ref ID, but not always"
    )
FlyBase Role of Gene in Wildtypetable fbRole
"Role of gene in wildType"
    (
    string geneId;	"FlyBase gene ID"
    int fbAllele;	"ID in fbAllele table or 0 if not allele-specific"
    int fbRef;		"ID in fbRef table"
    lstring text;	"Descriptive text"
    )
FlyReg Datatable flyreg
"Flyreg data from Casey Bergman"
    (
    string chrom;      "Chromosome"
    uint   chromStart; "Start position in chromosome"
    uint   chromEnd;   "End position in chromosome"
    string name;       "Factor"
    string target;     "Target"
    uint   pmid;       "PubMed ID"
    )
FlyReg Data (version 2)table flyreg
"Flyreg data (version 2) from Casey Bergman"
    (
    string chrom;      "Chromosome"
    uint   chromStart; "Start position in chromosome"
    uint   chromEnd;   "End position in chromosome"
    string name;       "Factor"
    string target;     "Target"
    uint   pmid;       "PubMed ID"
    uint   fpid;       "Footprint ID -- stable ID across versions"
    )
Fosmid End Pairstable fosEndPairs
"Positions of end pairs for fosmids"
   (
   short  bin;        	      "Bin number for browser speedup"
   string chrom;      	      "Chromosome"
   uint   chromStart; 	      "Start position of fosmid in chromosome"
   uint   chromEnd;   	      "End position of fosmid in chromosome"
   string name;       	      "Name of fosmid"
   uint   score;      	      "Score = 1000/(# of times fosmid appears in assembly)"
   char[1] strand;    	      "Value should be + or -"
   string pslTable;   	      "Table which contains corresponding PSL records for linked 
			       features"
   uint   lfCount;    	      "Number of linked features in the series"
   uint[lfCount]   lfStarts;  "Comma-separated list of start positions of each linked 
				feature in genomic"
   uint[lfCount]   lfSizes;   "Comma-separated list of sizes of each linked feature 
				in genomic"
   string[lfCount] lfNames;   "Comma-separated list of names of linked features"
   )
 Gap Positionstable chrN_gap
"Gaps in golden path"
    (
    ushort bin;         "A field to speed indexing added to many 
                         tables August 2001"
    uint   matches;     "Number of bases that match that aren't repeats"
    uint   misMatches;  "Number of bases that don't match"
    string chrom;       "which chromosome"
    uint   chromStart;  "start position in chromosome"
    uint   chromEnd;    "end position in chromosome"
    int    ix;          "ix of this fragment (useless)"
    char[1] n;          "always 'N'"
    uint   size;        "size of gap"
    string type;        "contig, clone, fragment, etc."
    string bridge;      "yes, no, mrna, bacEndPair, etc."
    )
GC Contenttable gcPercent
"Displays GC content in 20Kb non-overlapping blocks for genome"
   (
   string chrom;        "Chromosome number"
   uint   chromStart;   "Start position in chromosome"
   uint   chromEnd;     "End position in chromosome"
   string name;         "Constant string GC"
   uint   gcPpt;        "Average number of G and C per 1000 bases"
   )                                                                            
 GenBank Protein Annotationstable gbProtAnn
"Protein Annotations from GenPept mat_peptide fields"
    (
    string chrom;      	"Chromosome"
    uint   chromStart; 	"Start position in chromosome"
    uint   chromEnd;   	"End position in chromosome"
    string name;       	"Name of item"
    string product;    	"Protein product name"
    string note;       	"Note (may be empty)"
    string proteinId; 	"GenBank protein accession(.version)"
    uint giId;        	"GenBank db_xref number"
    )
Gene Bandstable geneBands
"Band locations of known genes"
   (
   string name;         "Gene name (HUGO Gene Nomenclature Committee symbol, if possible)"
   string mrnaAcc;      "RefSeq mRNA accession"
   int    count;        "Number of times this accession maps to the genome"
   string[count] bands; "List of chromosome bands to which it maps"
   )                                                                            
 Gene Boundaries as Defined by RNA and Spliced
EST Clusterstable rnaCluster
"Gene boundaries deduced from clustering spliced ESTs and mRNAs against the genome"
    (
    smallint bin;           "Index"
    string chrom;           "Chromosome or FPC contig"
    uint   chromStart;      "Start position in chromosome"
    uint   chromEnd;        "End position in chromosome"
    string name;            "Name of item"
    uint   score;           "Score from 0-1000"
    char[1] strand;         "+ or -"
    uint thickStart;        "Start of where display should be thick (start codon)"
    uint thickEnd;          "End of where display should be thick (stop codon)"
    uint reserved;          "Always zero for now"
    int blockCount;         "Number of blocks (a block contains no gaps)"
    longblob blockSizes;    "Size of each block"
    longblob chromStarts;   "Start position of each block in chromosome"
    ) 
Gene Predictions and RefSeq GenesThe following definition is used for gene prediction tables. In 
alternative-splicing situations, each transcript has a row in this table.table genePred
"A gene prediction."
    (
    string  name;               "Name of gene"
    string  chrom;              "Chromosome name"
    char[1] strand;             "+ or - for strand"
    uint    txStart;            "Transcription start position"
    uint    txEnd;              "Transcription end position"
    uint    cdsStart;           "Coding region start"
    uint    cdsEnd;             "Coding region end"
    uint    exonCount;          "Number of exons"
    uint[exonCount] exonStarts; "Exon start positions"
    uint[exonCount] exonEnds;   "Exon end positions"
    )
Gene Predictions (Extended)The following definition is used for extended gene prediction tables. In 
alternative-splicing situations, each transcript has a row in this table.table genePredExt
"A gene prediction with some additional info."
    (
    string name;        	"Name of gene (usually transcript_id from GTF)"
    string chrom;       	"Chromosome name"
    char[1] strand;     	"+ or - for strand"
    uint txStart;       	"Transcription start position"
    uint txEnd;         	"Transcription end position"
    uint cdsStart;      	"Coding region start"
    uint cdsEnd;        	"Coding region end"
    uint exonCount;     	"Number of exons"
    uint[exonCount] exonStarts; "Exon start positions"
    uint[exonCount] exonEnds;   "Exon end positions"
    uint id;            	"Unique identifier"
    string name2;       	"Alternate name (e.g. gene_id from GTF)"
    string cdsStartStat; 	"enum('none','unk','incmpl','cmpl')"
    string cdsEndStat;   	"enum('none','unk','incmpl','cmpl')"
    lstring exonFrames; 	"Exon frame offsets {0,1,2}"
    )
Gene Predictions and RefSeq Genes with Gene NamesA version of genePred that associates the gene name with the gene prediction 
information. In alternative splicing situations each transcript has a row in this table.table refFlat
"A gene prediction with additional geneName field."
    (
    string  geneName;           "Name of gene as it appears in Genome Browser."
    string  name;               "Name of gene"
    string  chrom;              "Chromosome name"
    char[1] strand;             "+ or - for strand"
    uint    txStart;            "Transcription start position"
    uint    txEnd;              "Transcription end position"
    uint    cdsStart;           "Coding region start"
    uint    cdsEnd;             "Coding region end"
    uint    exonCount;          "Number of exons"
    uint[exonCount] exonStarts; "Exon start positions"
    uint[exonCount] exonEnds;   "Exon end positions"
    )
Gene Predictions and RefSeq Genes Amino Acid TranslationsThe following definition is used for tables that link a predicted peptide to 
a predicted gene: acemblyPep, ECgenePep, ensPep, genieAltPep, genieKnownPep, 
genscanPep, knownGenePep, refPep, sanger22Pep, softberryPep, twinscanPep, vegaPep.table pepPred
"A predicted peptide linked to a predicted gene."
    (
    string  name;       "Name of gene - same as in genePred"
    lstring seq;        "Peptide sequence"
    )
GenMapDB BAC Clonestable genMapDb
"BAC clones from GenMapDB placed on the assembly by U Penn (V. Cheung)"
   (
   string  chrom;       "Chromosome number or 'unknown'"
   int     chromStart;  "Start position in chromosome (-1 if unpositioned)"
   int     chromEnd;    "End position in chromosome"
   string  name;        "Clone name"
   uint    score;       "Score - always 1000" 
   char[1] strand;      "+ or -"
   string  accT7;       "Accession number for T7 BAC end sequence"
   uint    startT7;     "T7 start position in chromosome"
   uint    endT7;       "T7 end position in chromosome"
   char[1] strandT7;    "+ or -"
   string  accSP6;      "Accession number for Sp6 BAC end sequence"
   uint    startSP6;    "Sp6 start position in chromosome"
   uint    endSP6;      "Sp6 end position in chromosome"
   char[1] strandSP6;   "+ or -"
   string  stsMarker;   "Name of STS marker found in clone"
   uint    stsStart;    "STS marker start position in chromosome" 
   uint    stsEnd;      "STS marker end position in chromosome"
   )                                                                            
 Golden Path Constructiontable chrN_gold
"How to get through chromosome based on fragments"
    (
    ushort  bin;        "A field to speed indexing added to many 
                         tables August 2001"
    uint    matches;    "Number of bases that match that aren't repeats"
    uint    misMatches; "Number of bases that don't match"
    string  chrom;      "Which chromosome"
    uint    chromStart; "Start position in chromosome"
    uint    chromEnd;   "End position in chromosome"
    int     ix;         "Ix of this fragment (useless)"
    char[1] type;       "(P)redraft, (D)raft, (F)inished or (O)ther"
    string  frag;       "Which fragment"
    uint    fragStart;  "Start position in frag"
    uint    fragEnd;    "End position in frag"
    char[1] strand;     "+ or - (orientation of fragment)"
    )
H-Invitational Human Gene Annotation Database Datatable HInv
"H-Invitational gene data"
    (
    string geneId; 	"Gene ID"
    string clusterId;	"Gene cluster ID"
    string mrnaAcc; 	"GenBank mRNA accession"
    )
HgFind Search Informationtable hgFindSpec
"Defines a search to be performed by hgFind"
    (
    string searchName;          "Unique name for this search. Defaults to searchTable 
				 if not specified in .ra"
    string searchTable;         "(Non-unique!) Table to be searched. (Like trackDb.tableName: 
				 if split, omit chr*_ prefix)"
    string searchMethod;        "Type of search (exact, prefix, fuzzy)"
    string searchType;          "Type of search (bed, genePred, knownGene etc)"
    ubyte shortCircuit;         "If nonzero and there is a result from this search, jump 
				 to the result instead of performing other searches"
    string termRegex;           "Regular expression (see man 7 regex) to eval on search 
				 term: if it matches, perform search query"
    string query;               "sprintf format string for SQL query on a given table 
				 and value"
    string xrefTable;           "If search is xref, perform xrefQuery on search term, 
				 then query with that result"
    string xrefQuery;           "sprintf format string for SQL query on a given (xref) 
				 table and value"
    float searchPriority;       "0-1000 - relative order/importance of this search.  
				 0 is top"
    string searchDescription;   "Description of table/search (default: trackDb 
				 {longLabel,tableName})"
    lstring searchSettings;     "Name/value pairs for searchType-specific stuff"
)
Hugo Gene Nomenclature Committee (HGNC) Cross-Referencetable hugo
"A cross-reference table between HGNC and other databases"
   (
   string hgnc;            "HGNC number"
   string symbol;          "HGNC gene symbol"
   string name;            "HGNC gene name"
   string map;             "Gene map location"
   string mim;             "MIM ID"
   string pmid1;           "pmid 1"
   string pmid2;           "pmid 2"
   string refseq;          "RefSeq ID"
   string aliases;         "Aliases"
   string widthdraws;      "Withdrawn gene symbols"
   string locuslink;       "LocusLink ID"
   string gdbID;           "GDB ID"
   string swissprot;       "UniProtKB ID"
   )
 Human Synteny Alignmentstable syntenyHuman
"Human synteny alignnments from blastz single coverage"
    (
    string chrom;       "Mouse Chrom"
    uint chromStart;    "Start on Mouse"
    uint chromEnd;      "End on Mouse"
    string name;      	"Human Chromosome"
    uint score;         "Score (always zero)"
    char[1] strand;     "+ direction matches - opposite"
    uint thickStart;    "Start of where display should be thick"
    uint thickEnd;      "End of where display should be thick"
    )
ImageClonetable imageClone
"Used with image consortium's cumulative_plate files: ftp://image.llnl.gov/image/outgoing"
    (
    uint id; 			"IMAGE clone ID"
    string library; 		"Clone collection (LLAM for amp-resistant libraries,
				 LLCM for chloramphenicol-resistant libraries, LLKM
				 for kanamycin-resistant libraries.  No rearray 
				 locations are given.)"
    uint plateNum; 		"Plate number"
    string row; 		"Row"
    uint column; 		"Column"
    uint libId; 		"IMAGE library ID"
    string organism; 		"Species"
    int numGenbank; 		"Number of GenBank records"
    string[numGenbank] genbankIds; "GenBank accession number(s)"
    )
InterPro Cross Referencetable interProXref
"A cross-reference table for InterPro."
        (
        string accession;       "UniProtKB accession number"
        string method;          "Method"
        int start;              "Start position"
        int end;                "End position"
        string interProId;      "InterPro ID"
        string description;     "Description"
        )
Jackson Lab Mouse Orthologstable jaxOrtholog
"Jackson Lab Mouse Orthologs"
    (
    string humanSymbol;	"Human HUGO Gene Nomenclature Committee symbol"
    string humanBand;   "Human chromosomal location"
    string mgiId;       "Mouse database id"
    string mouseSymbol; "Mouse human symbol"
    string mouseChr;    "Mouse chromosome"
    string mouseCm;     "Mouse genetic map positionin centimorgans"
    string mouseBand;   "Mouse chromosome band if any"
    )
Jackson Lab Quantitative Trait Locitable jaxQTL
"Quantitative Trait Loci from Jackson Lab/Mouse Genome Informatics"
    (
    string chrom;       "Human chromosome or FPC contig"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "Name of item"
    uint   score;       "Score from 0-1000 (bed6 compat.)"
    char[1] strand;     "+ or - (bed6 compat.)"
    string marker;      "MIT SSLP Marker w/highest correlation"
    string mgiID;       "MGI ID"
    string description; "MGI description"
    float  cMscore;     "cM position of marker associated with peak LOD score"
    )
Kegg Pathway Map Descriptiontable keggMapDesc
"Description of KEGG pathway map"
   (
   string mapID;        "KEGG pathway map ID"
   string description;  "KEGG pathway map description"
   )
 Kegg Pathway Cross Referencetable keggPathway
"Associates KEGG pathway IDs with Known Genes and LocusLink IDs"
   (
   string kgID;         "Known Gene ID"
   string locusID;      "LocusLink ID"
   string mapID;        "KEGG pathway map ID"
   )
 Known Canonicaltable knownCanonical
"Describes the canonical splice variant of a gene"
     (
     string chom;        "Chromosome"
     int chromStart;     "Start position (0 based). Corresponds to txStart"
     int chromEnd;       "End position (non-inclusive). Corresponds to txEnd"
     int clusterId;      "Which cluster of transcripts this belongs to in knownIsoforms"
     string transcript;  "Corresponds to knownGene name field"
     string protein;     "UniProtKB ID of associated protein"
     )
Known Genestable knownGene
"Protein coding genes based on proteins from UniProtKB 
and their corresponding mRNAs from GenBank"
    (
    string  name;               "Name of gene"
    string  chrom;              "Chromosome name"
    char[1] strand;             "+ or - for strand"
    uint    txStart;            "Transcription start position"
    uint    txEnd;              "Transcription end position"
    uint    cdsStart;           "Coding region start"
    uint    cdsEnd;             "Coding region end"
    uint    exonCount;          "Number of exons"
    uint[exonCount] exonStarts; "Exon start positions"
    uint[exonCount] exonEnds;   "Exon end positions"
    string  proteinID;          "UniProtKB ID" 
    string  alignID;            "Unique identifier for each (known gene, alignment 
                                 position) pair"
    )
Known Genes Aliastable kgAlias
"Links together a Known Gene ID and a gene alias"
    (
    string kgID;        "Known Gene ID"
    string alias;	"A gene alias"
    )
Known Genes Associations
The following definition describes tables that associate Known Genes with other 
IDs and accessions.
 table knownTo
"Maps Known Gene to another ID"
    (
    string name;        "Same as name field in known gene"
    string value;       "Other id"
    )
Known Genes Cross Referencetable kgXref
"Links a Known Gene ID with mRNA, UniProtKB, RefSeq, and NCBI accessions/IDs"
    (
    string kgID;        "Known Gene ID"
    string mRNA;        "mRNA ID"
    string spID;        "UniProtKB protein Accession number"
    string spDisplayID; "UniProtKB display ID"
    string geneSymbol;  "Gene Symbol"
    string refseq;      "RefSeq ID"
    string protAcc;     "NCBI protein Accession number"
    string description; "Description"
    )
Known Genes Isoforms
The following definition describes tables that link together various transcripts 
of a gene into a cluster.
 table knownIsoforms
"Links together various transcripts of a gene into a cluster"
    (
    int clusterId;      "Unique id for transcript cluster (aka gene)"
    string transcript;  "Corresponds to name in knownGene table, transcript in 
			 knownCanonical"
    )
Known Genes Linktable knownGeneLink
"Known Genes link table, currently storing DNA-based entries only"
    (
    string  name;       "Known Genes ID"
    char[1] seqType;    "Known Genes sequence type - mRNA-base genes=m, DNA-based genes=g"
    string  proteinID;  "Corresponding protein ID"
    )
Known Genes Protein Aliastable kgProtAlias
"Links together a Known Gene ID and a protein alias"
    (
    string kgID;        "Known Gene ID"
    string displayID;	"protein display ID"
    string alias;	"A protein alias"
    )
Known Genes Superfamily Linktable knownToSuper
"Maps protein superfamilies to known genes"
    (
    string gene;	"Known gene ID"
    int superfamily;	"Superfamily ID"
    int start;		"Start of superfamily domain in protein (0 based)"
    int end;		"End (noninclusive) of superfamily domain"
    float eVal;		"E value of superfamily assignment"
    )
Known Genes UniProtKB Aliastable kgSpAlias
"Links together a Known Gene ID and a protein alias"
    (
    string kgID;        "Known Gene ID"
    string spID;	"UniProtKB protein accession number"
    string alias;	"Alias - could be either a gene alias or protein alias"
    )
Known (RefSeq) Genes IDs in Other DatabasesLast used Oct. 2000
 
 table knownMore 
"Lots of auxiliary info about a known gene" 
    (  
    string name;	  "The name displayed in the browser:
                           OMIM, gbGeneName, or transId"   
    string transId;       "Transcript ID. Genie-generated ID" 
    string geneId;        "Gene (not transcript) Genie ID"   
    uint   gbGeneName;    "Connect to geneName table. GenBank gene name"   
    uint   gbProductName; "Connects to productName table. GenBank product name" 
    string gbProteinAcc;  "GenBank accession of protein"  
    string gbNgi;         "GenBank GI of nucleotide sequence" 
    string gbPgi;         "GenBank GI of protein sequence"   
    uint   omimId;        "OMIM ID or 0 if none"  
    string omimName;      "OMIM primary name"  
    uint   hugoId;        "HUGO Gene Nomeclature Committee (HGNC) ID, or 0 if none" 
    string hugoSymbol;    "HGNC short name"  
    string hugoName;      "HGNC descriptive name" 
    string hugoMap;       "HGNC Map position" 
    uint   pmId1;         "Data from HGNC nomeids.txt" 
    uint   pmId2;         "Data from HGNC nomeids.txt"
    string refSeqAcc;     "Accession of RefSeq mRNA" 
    string aliases;       "Aliases, if any.  Comma and space separated list" 
    uint   locusLinkId;   "Locus link ID" 
    string gdbId;         "NCBI GDB database ID" 
    )
Known (RefSeq) Genes - Other InformationLast used Oct. 2000table knownInfo
"Auxiliary info about a known gene"
    (
    string name;         "Connects with genieKnown->name"
    string transId;      "Transcript id. Genie-generated ID"
    string geneId;       "Gene (not transcript) ID"
    uint   geneName;     "Connect to geneName table"
    uint   productName;  "Connects to productName table"
    string proteinId;    "GenBank accession of protein?"
    string ngi;          "GenBank gi of nucleotide seq"
    string pgi;          "GenBank gi of protein seq"
    )
MGC Full Statustable mgcFullStatus
"Status of MGC clone"
    (
    uint imageId;    	"Image ID for clone"
    enum status;	"MGC status code: unpicked, picked, notBack, noDecision,
			 fullLength, incomplete, chimeric, frameShift, contaminated,
			 retainedIntron, mixedWells, noGrowth, noInsert, no5est,
			 microDel, artifact, noPolyATail, or cantSequence. Status will
			 always be fullLength on main databases."
    char acc;		"GenBank accession"
    char organism;    	"Two-letter MGC organism" 
    )
MGI IDtable MGIid
"Links MGI ID to Locus Link ID (Mouse)"
    (
    char[8]  LLid;       "Locus Link ID"
    char[12] MGIid;      "MGI ID"
    char[32] symbol;     "Symbol"
    )
Microsatellites from Gerome Breen's VNTR Program"table vntr
"Microsatellites from Gerome Breen's VNTR program"
    (
    string chrom;      		"chrom"
    uint   chromStart; 		"Start position in chromosome"
    uint   chromEnd;   		"End position in chromosome"
    string name;       		"Name of item (Repeat unit)"
    float  repeatCount; 	"Number of perfect repeats"
    int distanceToLast; 	"Distance to previous microsat. repeat"
    int distanceToNext; 	"Distance to next microsat. repeat"
    string forwardPrimer; 	"Forward PCR primer sequence (or Design_Failed)"
    string reversePrimer; 	"Reverse PCR primer sequence (or Design_Failed)"
    string pcrLength;     	"PCR product length (or Design_Failed)"
    )
Mouse SyntenyLast used Apr. 2001.table mouseSyn
"Synteny between mouse and human chromosomes."
    (
    string  chrom;       "Name of chromosome"
    uint    chromStart;  "Start in chromosome"
    uint    chromEnd;    "End in chromosome"
    string  name;        "Name of mouse chromosome"
    int     segment;     "Number of segment"
    )
Mouse Synteny Alignmentstable syntenyMouse
"Mouse synteny alignnments from blastz single coverage"
    (
    string chrom;       "Human chromosome"
    uint chromStart;    "Start on human chromosome"
    uint chromEnd;      "End on human chromosome"
    string name;  	"Mouse chromosome"
    uint score;         "Score (always zero)"
    char[1] strand;     "+ (direction matches) or - (opposite direction)"
    uint thickStart;    "Start of where display should be thick"
    uint thickEnd;      "End of where display should be thick"
    )
Mouse Synteny (Whitehead)table mouseSynWhd
"Whitehead synteny between mouse and human chromosomes."
    (
    string  chrom;       "Human chromosome"
    uint    chromStart;  "Start position in human chromosome"
    uint    chromEnd;    "End position in human chromosome"
    string  name;        "Name of mouse chromosome"
    uint    score;       "Unused (bed 6 compatibility)"
    char[1] strand;      "+ or - (orientation of fragment)"
    uint    mouseStart;  "Start position in mouse chromosome"
    unit    mouseEnd;    "End position in mouse chromosome"
    string  segLabel;    "Whitehead segment label"
    )
mRNA Sequencestable mrnaPred
"A mRNA - linked to a gene."
    (
    string  name;       "Name of gene - same as in genePred"
    lstring seq;        "mRNA sequence"
    )
mrnaRefSeqtable mrnaRefseq
"Associates mRNA IDs with RefSeq IDs"
    (
    string  mrna;       "mRNA ID"
    string  refseq;     "RefSeq ID"
    )
mRNA/EST/Blat AlignmentsThe following definition is used for the blat and blastz tables, EST tables, mRNA
tables, dbtssAli, and uniGene.
 
 table psl  
"Summary info about a patSpace alignment" 
    ( 
    ushort  bin;          	  "A field to speed indexing" 
    uint    matches;      	  "Number of bases that match that aren't repeats"
    uint    misMatches;   	  "Number of bases that don't match"  
    uint    repMatches;   	  "Number of bases that match but are part of repeats" 
    uint    nCount;       	  "Number of 'N' bases" 
    uint    qNumInsert;   	  "Number of inserts in query" 
    int     qBaseInsert;  	  "Number of bases inserted in query" 
    uint    tNumInsert;   	  "Number of inserts in target" 
    int     tBaseInsert;  	  "Number of bases inserted in target"
    char[2] strand;       	  "+ or - for query strand. For translated alignments, 
				   second +/- is for genomic strand"  
    string  qName;        	  "Query sequence name"
    uint    qSize;        	  "Query sequence size"
    uint    qStart;       	  "Alignment start position in query"
    uint    qEnd;         	  "Alignment end position in query" 
    string  tName;        	  "Target sequence name" 
    uint    tSize;        	  "Target sequence size" 
    uint    tStart;       	  "Alignment start position in target" 
    uint    tEnd;         	  "Alignment end position in target" 
    uint    blockCount;   	  "Number of blocks in alignment (a block contains no gaps)" 
    uint[blockCount] blockSizes;  "Size of each block" 
    uint[blockCount] qStarts;     "Start of each block in query" 
    uint[blockCount] tStarts;     "Start of each block in target"
    )  
There is a little gotcha in this table format. It has to 
do with how coordinates are handled on the negative strand.
In the qStart/qEnd fields the coordinates are where it
matches from the point of view of the forward strand 
(even when the match is on the reverse strand). However
on the qStarts[] list, the coordinates are reversed. 
Here's an example of a 30-mer that has 2 blocks that
align on the minus strand and 2 blocks on the plus
strand (these types of situations happen in real life in
response to assembly errors sometimes).
 
 
| 0         1         2         3 tens position in query    |  | 0123456789012345678901234567890 ones position in query    |  |             ++++          +++++ plus strand alignment on query    |  |     --------    ----------      minus strand alignment on query    |  |  |  | Plus strand:    |  |      qStart 12 qEnd 31 blockSizes 4,5 qStarts 12,26    |  | Minus strand:    |  |      qStart 4 qEnd 26 blockSizes 10,8 qStarts 5,19     |  Essentially the minus strand blockSizes and qStarts are 
what you would get if you reverse complemented the query.
However the qStart and qEnd are non-reversed. To get
from one to the other:
 
     qStart = qSize - revQEnd
     qEnd = qSize - revQStart
Net Alignmentstable netAlign
"Database representation of a net of alignments"
   (
   uint level;       "Level of alignment"
   string tName;     "Target chromosome"
   uint tStart;      "Start on target"
   uint tEnd;        "End on target"
   char[1] strand;   "Orientation of query (+ or -)"
   string qName;     "Query chromosome"
   uint qStart;      "Start on query"
   uint qEnd;        "End on query"
   uint chainId;     "Associated chain ID with alignment details"
   uint ali;         "Bases in gap-free alignments"
   double score;     "Score - a number proportional to 100x matching bases"
   int qOver;        "Overlap with parent gap on query side (-1 for undefined)"
   int qFar;         "Distance from parent gap on query side ( -1 for undefined)"
   int qDup;         "Bases with two or more copies in query ( -1 for undefined)"
   string type;      "Syntenic type: gap/top/syn/nonsyn/inv"
   int tN;           "Unsequenced bases on target (-1 for undefined)"
   int qN;           "Unsequenced bases on query (-1 for undefined)"
   int tR;           "RepeatMasker bases on target (-1 for undefined)"
   int qR;           "RepeatMasker bases on query (-1 for undefined)"
   int tNewR;        "Lineage specific repeats on target (-1 for undefined)"
   int qNewR;        "Lineage specific repeats on query (-1 for undefined)"
   int tOldR;        "Bases of ancient repeats on target (-1 for undefined)"
   int qOldR;        "Bases of ancient repeats on query (-1 for undefined)"
   int tTrf;         "Bases of tandam repeats on target (-1 for undefined)"
   int qTrf;         "Bases of tandam repeats on query (-1 for undefined)"
   )
 Non-standard Join Certificatestable certificate
"Non-standard Join Certificates"
   (
   string accession1; 	"First accession number"
   string accession2; 	"Second accession number"
   string spanner; 	"Spanner"
   string evaluation; 	"Evaluation"
   string variation; 	"Variation"
   string varEvidence; 	"Variation evidence"
   string contact; 	"Contact info"
   string remark; 	"Remarks"
   string comment; 	"Comments"
   )
 Orientation InfoThe following definition is used by the mrnaOrientInfo and estOrientInfo 
tables. It contains extra information on mRNAs/ESTs calculated by the 
polyInfo program.table estOrientInfo
"Extra information on mRNAs/ESTs calculated by polyInfo program"
   (
   int    bin;               "A field to speed indexing"
   uint   chromStart;        "Start position in chromosome"
   uint   chromEnd;          "End position in chromosome"
   string name;              "Accession of EST/mRNA"
   short intronOrientation;  "Orientation of introns with respect to EST/mRNA"
   short sizePolyA;          "Number of trailing A's"
   short revSizePolyA;       "Number of trailing A's on reverse strand"
   short signalPos;          "Position of start of polyA signal relative to end 
	                         of EST/mRNA, or 0 if no signal"
   short revSignalPos;       "PolyA signal position on reverse strand if any"
   )
 Pfam Descriptiontable pfamDesc 
"Pfam description table"
   (
   string pfamAC;          "Pfam accession number"
   string pfamID;          "Pfam ID"
   string description;     "Description"
   )
 Pfam and UniProtKB Cross Referencetable pfamXref
"A cross-reference table between Pfam ID and UniProtKB IDs."
   (
   string pfamAC;          "Pfam accession number"
   string swissAC;         "UniProtKB accession number"
   string swissDisplayID;  "UniProtKB display ID"
   )
 Proteome Browser Amino Acid Distributiontable pbAaDistX
"Distribution for a specific amino acid X"
   (
   float x; "x value"
   float y; "count"
   )
 Proteome Browser Amino Acid Anomaly Limitstable pbAnomLimit
"Protein amino acid anomaly limits for each AA"
   (
   char[1] AA;          "Amino Acid"
   float   pctLow;      "Percentage (100%=1.0) Lower bound"
   float   pctHi;       "Percentage (100%=1.0) Upper bound"
   )
 Proteome Browser Cysteine Count Distributiontable pepCCntDist
"Cysteine count distribution"
   (
   float x;             "Number of Cysteines"
   float y;             "Count of proteins with x Cysteines"
   )
 Proteome Browser Exon Count Distributiontable pepExonCntDist
"Exon count distribution"
   (
   float x;             "Number of exon"
   float y;             "Count of proteins with x exons"
   )
 Proteome Browser Hydrophobicity Distributiontable pepHydroDist
"Hydrophobicity distribution"
   (
   float x;             "Hydrophobicity value"
   float y;             "Count of proteins with hydrophobicity near x"
   )
 Proteome Browser InterProt Domain Count Distributiontable pepIPCntDist
"InterProt domain count distribution"
   (
   float x;             "Number of InterPro domains"
   float y;             "Count of proteins with x InterPro domains" 
   )
 Proteome Browser Molecular Weight and AA Length of Proteinstable pepMwAa 
"Molecular weight and AA length of proteins"
   (
   string accession;    "UniProtKB protein accession number"
   float  molWeight;    "Molecular weight" 
   int    aaLen;        "Length of protein sequence"
   )
 Proteome Browser Molecular Weight Distributiontable pepMolWtDist
"Molecular weight distribution"
   (
   float x;             "Molecular weight value"
   float y;             "Count of proteins with molecular weight near x"
   )
 Proteome Browser pI Distributiontable pepPiDist
"pI distribution" 
   (
   float x;             "pI  value" 
   float y;             "Count of proteins with pI value near x"
   )
 Proteome Browser Predicted Peptide/Predicted Genetable pepPred
"Predicted peptide linked to predicted gene"
    (
    string name;        "Name of gene - same as in genePred"
    lstring seq;        "Peptide sequence" 
    )
Proteome Browser Protein pIstable pepPi
"Protein pIs" 
   (
   string accession;     "Protein accession number" 
   float pI;             "pI value"
   )
 Proteome Browser Residue Average/Standard Deviationtable pbResAvgStd
"Residue average and standard deviation"
   (
   char[1] residue;     "Protein residue"
   float   avg;         "Average"
   float   stddev;      "Standard deviation"
   )
 Proteome Browser Residue Distributiontable pepResDist
"Residue distribution" 
   (
   float x;             "Residue index (WCMHYNFIDQKRTVPGEASL) "
   float y;             "Count of proteins with residue index of x"
   )
 Proteome Browser Stamp Informationtable pbStamp
"Info needed for a Proteome Browser stamp"
    (
    char[40] stampName; 	"Short Name of stamp"
    char[40] stampTable;	"Database table name of the stamp (distribution) data"
    char[40] stampTitle;	"Stamp Title to be displayed"
    int len;            	"Number of x-y pairs"
    float  xmin;        	"x minimum"
    float  xmax;        	"x maximum"
    float  ymin;        	"y minimum"
    float  ymax;        	"y maximum"
    string stampDesc;   	"Description of the stamp"
    )
PDB and UniProtKB ID linkstable pdbSP
"A cross-reference table between UniProtKB accession IDs and PDB IDs."
    (
    string pdb;             "PDB ID"
    string sp;              "UniProtKB display ID"
    )
P-Screen Data (BDGP Gene Disruption Project)table pscreen
"P-Screen (BDGP Gene Disruption Project) P el. insertion locations/genes"
    (
    string chrom;      		"Chromosome"
    uint   chromStart; 		"Start position in chromosome"
    uint   chromEnd;   		"End position in chromosome"
    string name;       		"Name of item (mutant strain with P el. insert here)"
    uint   score;      		"Score from 0-1000 (placeholder! for bed 6 compat)"
    char[1] strand;    		"+ or -"
    uint stockNumber;  		"Mutant strain stock number, for ordering"
    uint geneCount;    		"Number of genes disrupted by this insert"
    string[geneCount] geneIds;  "IDs of disrupted genes"
    )
Pseudogene Link to Ortholog/Paralog
table pseudoGeneLink
"Links a gene/pseudogene prediction to an ortholog or paralog."
    (
    string chrom;       	 "Chromosome name for pseudogene"
    uint chromStart;    	 "Pseudogene alignment start position"
    uint chromEnd;      	 "Pseudogene alignment end position"
    string name;        	 "Name of pseudogene"
    uint score;         	 "Score of pseudogene with gene"
    char[2] strand;     	 "+ or -"
    uint thickStart;    	 "Start of where display should be thick (start codon)"
    uint thickEnd;      	 "End of where display should be thick (stop codon)"
    uint reserved;      	 "Always zero for now"
    int blockCount;     	 "Number of blocks (a block contains no gaps)"
    int[blockCount] blockSizes;  "Comma-separated list of block sizes"
    int[blockCount] chromStarts; "Start positions relative to chromStart"
    float trfRatio;     	 "Ratio of tandem repeats"
    string type;        	 "Type of evidence"
    int axtScore;       	 "Blastz score, gene mRNA aligned to pseudogene"
    string gChrom;      	 "Chromosome name"
    int gStart;         	 "Gene alignment start position"
    int gEnd;           	 "Gene alignment end position"
    char[2] gStrand;    	 "Strand of gene"
    uint exonCount;     	 "# of exons in gene "
    uint geneOverlap;   	 "Bases overlapping"
    uint polyA;         	 "Length of polyA"
    int polyAstart;     	 "Start of polyA relative to end of pseudogene"
    uint exonCover;     	 "Number of exons in gene covered"
    uint intronCount;   	 "Number of introns in pseudogene"
    uint bestAliCount;  	 "Number of good mRNAs aligning"
    uint matches;       	 "Matches + repMatches"
    uint qSize;         	 "Aligning bases in pseudogene"
    uint qEnd;          	 "End of cDNA alignment"
    uint tReps;         	 "Repeats in gene"
    uint qReps;         	 "Repeats in pseudogene"
    uint overlapDiag;   	 "Bases on the diagonal to mouse"
    uint coverage;      	 "Bases on the diagonal to mouse"
    int label;          	 "1=pseudogene,-1 not pseudogene"
    uint milliBad;      	 "MilliBad score, pseudogene aligned to genome"
    uint oldScore;      	 "Another heuristic"
    int oldIntronCount; 	 "Old simple intron count"
    int conservedIntrons; 	 "Conserved intron count"
    string intronScores; 	 "Intron sizes in gene/pseudogene"
    int maxOverlap ;    	 "Largest overlap with another mRNA"
    string refSeq;      	 "Name of closest RefSeq to gene"
    int rStart;         	 "RefSeq alignment start position"
    int rEnd;           	 "RefSeq alignment end position"
    string mgc;         	 "Name of closest MGC to gene"
    int mStart;         	 "MGC alignment start position"
    int mEnd;           	 "MGC alignment end position"
    string kgName;      	 "Name of closest Known Gene to gene"
    int kStart;         	 "Known Gene alignment start position"
    int kEnd;           	 "Known Gene alignment end position"
    string overName;    	 "Name of overlapping mrna"
    int overStart;      	 "Overlapping mRNA start position"
    int overEnd;       		 "Overlapping mRNA end position"
    char[2] overStrand;  	 "Strand of overlapping mRNA"
    int adaBoost;       	 "AdaBoost label"
    float posConf;      	 "P-value for positive"
    float negConf;      	 "P-value for positive"
    )
RankProp Scoretable rankProp
"RankProp protein ranking for a pair of proteins"
    (
    string query;       "Known Genes ID of query protein"
    string target;      "Known Genes ID of target protein"
    float score;        "Rankp score"
    )
Rat Synteny Alignments table syntenyRat
"Rat synteny alignnments from blastz single coverage"
    (
    string chrom;       "Human chromosome"
    uint chromStart;    "Start on human chromosome"
    uint chromEnd;      "End on human chromosome"
    string name;    	"Rat chromosome"
    uint score;         "Score (always zero)"
    char[1] strand;     "+ (direction matches) or - (opposite direction)"
    uint thickStart;    "Start of where display should be thick"
    uint thickEnd;      "End of where display should be thick"
    )
Recombination Ratetable recombRate
"Describes the recombination rate in 1Mb intervals based on deCODE, Marshfield and
 Genethon maps"
    (
    string  chrom;            "Chromosome number"
    uint    chromStart;       "Start position in genoSeq"
    uint    chromEnd;         "End position in genoSeq"
    string  name;             "Constant string 'recombRate'"
    float   decodeAvg;        "Calculated deCODE Sex-averaged rate from map"
    float   decodeFemale;     "Calculated deCODE female recombination rate"
    float   decodeMale;       "Calculated deCODE male recombination rate"
    float   marshfieldAvg;    "Calculated Marshfield recombination rate"
    float   marshfieldFemale; "Calculated Marshfield female recombination"
    float   marshfieldMale;   "Calculated Marshfield male recombination rate"
    float   genethonAvg;      "Calculated Genethon recombination rate"
    float   genethonFemale;   "Calculated Genethon female recombination rate"
    float   genethonMale;     "Calculated Genethon male recombination rate"
    )
RefSeq LinkFirst used Dec. 2000table refLink
"Link between RefSeq mRNAs and HUGO Gene Nomenclature Committee, LocusLink etc."
    (
    string name;        "Name displayed in UI"
    string product;     "Name of protein product"
    string mrnaAcc;     "mRNA accession"
    string protAcc;     "Protein accession"
    uint geneId;        "Pointer to geneName table"
    uint prodId;        "Pointer to prodName table"
    uint locusLinkId;   "Locus Link ID"
    uint omimId;        "OMIM ID"
    )
RefSeq StatusFirst used Dec. 2001table refSeqStatus
"Links RefSeq mRNA accessions with status"
    (
    string mrnaAcc;     "RefSeq mRNA accession"
    string status;      "RefSeq status (Reviewed, Provisional, Predicted)"
    )
RefSeq SummaryFirst used Oct. 2003table refSeqStatus
"Sparse summary table created for refSeqs with "Summary:" or "COMPLETENESS:" in comment"
    (
    string mrnaAcc; 	"RefSeq mRNA accession"
    enum completeness; 	"Level of completeness: Unknown, Complete5End, 
			Complete3End, FullLength, IncompleteBothEnds, 
			Incomplete5End, Incomplete3End, Partial"
    string summary;	"Summary text"
    )
Regulatory Module TFBS Predictions (Eran Segal)table esRegGeneToMotif
"Browser extensible data with gene field"
    (
    string    chrom;      "Chromosome"
    uint      chromStart; "Start position in chromosome"
    uint      chromEnd;   "End position in chromosome"
    string    name;       "Motif name"
    uint      score;      "Score from 0-1000"
    char[1]   strand;     "+ or -"
    varchar   gene;    	  "Gene name"
    )
Repeating ElementsTable created from RepeatMasker .out files.table rmsk
"RepeatMasker .out record"
    (
    uint swScore;       "Smith Waterman alignment score"
    uint milliDiv;      "Base mismatches in parts per thousand"
    uint milliDel;      "Bases deleted in parts per thousand"
    uint milliIns;      "Bases inserted in parts per thousand"
    string genoName;    "Genomic sequence name"
    uint genoStart;     "Start in genomic sequence"
    uint genoEnd;       "End in genomic sequence"
    int  genoLeft;      "Size left in genomic sequence"
    char[1] strand;     "Relative orientation + or -"
    string repName;     "Name of repeat"
    string repClass;    "Class of repeat"
    string repFamily;   "Family of repeat"
    int repStart;       "Start in repeat sequence"
    uint repEnd;        "End in repeat sequence"
    int repLeft;        "Size left in repeat sequence"
    char[1] id;         "First digit of id field in RepeatMasker .out file. Best ignored."
    )
Riken Altid Tabletable rikenaltid
"Riken altid table"
    (
    char[64]    ID;             "ID (composite)"
    char[32]    SeqID;          "Sequence ID"
    char[32]    AltIDType;      "Alternate ID type"
    string      AltID;          "Alternate ID"
    )
Riken Annotation Tabletable rikenann
"Riken annotation table"
    (
    string  ID;             "ID"
    string  seqid;          "parent sequence id"
    uint    i;              "sequential number"
    string  Qualifier;      "Qualifier"
    string  Anntext;        "Anntext"
    string  Datasrc;        "Datasrc"
    string  Srckey;         "Srckey"
    string  Href;           "xlink_href"
    string  Evidence;       "Evidence"
    )
Riken Cluster Tabletable rikencluster
"Riken cluster table"
    (
    string  ID;                     "ID"
    string  Fantomid;               "Famtom"
    string  RepresentativeSeqid;    "Representative sequence ID"
    uint    Nsequence;              "Number of Sequencesse"
    )
Riken Cluster Sequence Regulation Tabletable rikenclusterseq
"Riken cluster sequence regulation table"
    (
    string  ClusterID;              "Cluster ID"
    string  SeqID;                  "Sequence ID"
    )
Riken Sequence Tabletable rikenseq
"Riken sequence table"
    (
    string  ID;             "ID"
    uint    Naltid;         "Number of altid"
    string  Seqid;          "sequence ID (no more valid per Riken DTD)"
    string  Fantomid;       "Fantom ID (no more valid per Riken DTD)"
    string  Cloneid;        "Clone ID (no more valid per Riken DTD)"
    string  Rearrayid;      "Rearray ID (no more valid per Riken DTD)"
    string  Accession;      "Accession (no more valid per Riken DTD)"
    string  Annotator;      "Annotator"
    string  version;        "Version"
    string  ModifiedTime;   "Modified Time"
    uint    Nannotation;    "Number of Annotations"
    string  Comment;        "Comment"
    )
RNA Folding Infotable rnaFold
"Info about folding of RNA into secondary structure"
    (
    string name;	"mRNA accession"
    lstring seq;	"mRNA sequence (U's instead of T's)"
    lstring fold;	"Parenthesis and .'s that describe folding"
    float energy;	"Estimated free energy of folding (negative)"
    )
RNA Gene PositionsLast used Apr. 2001.table rnaGene
"Describes functional RNA genes."
    (
    string  chrom;        "Chromosome gene is on"
    uint    chromStart;   "Start position in chromosome"
    uint    chromEnd;     "End position in chromosome"
    string  name;         "Name of gene"
    uint    score;        "Score from 0 to 1000"
    char[1] strand;       "Strand: + or -"
    string  source;       "Source as in Sean Eddy's files."
    string  type;         "Type - snRNA, rRNA, tRNA, etc."
    float   fullScore;    "Score as in Sean Eddy's files."
    ubyte   isPsuedo;     "TRUE(1) if psuedo, FALSE(0) otherwise"
    )
RNA - Weber and Griffiths-Jonestable wgRna
"CD and H/ACA Box snoRNAs and microRNAs from Weber and Griffiths-Jones"
    (
    string  chrom;        "Chromosome"
    uint    chromStart;   "Start position in chromosome"
    uint    chromEnd;     "End position in chromosome"
    string  name;         "Name of item"
    uint    score;        "Score from 0 to 1000 (bed6 compat.)"
    char[1] strand;       "+ or - (bed6 compat.)"
    uint    thickStart;   "Start of thick region"
    uint    thickEnd;     "End of thick region"
    string  type;         "RNA type"
    }
Rosetta Information table rosettaExps
"Rosetta Experimental Confirmation information"
    (
    int	      ID;        	
    string    name;   	
    longblob  description;
    longblob  URL;       
    longblob  ref;      
    longblob  credit;  
    uint      numExtras;
    longblob  extra;   
    )                                                                         
Saccharomyces Genome Database Protein Abundancetable sgdAbundance
"Protein abundance data from http://yeastgfp.ucsf.edu via SGD"
    (
    string name;        "ORF name in sgdGene table"
    float abundance;    "Absolute abundance from 41 to 1590000"
    string error;       "Error - either a floating point number or blank"
    )
Saccharomyces Genome Database Clone Informationtable sgdClone
"Clone info from yeast genome database"
    (
    string chrom;       "Chromosome in chrN format"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "Washington University name"
    string atccName;    "ATCC clone name (optional)"
    )
Saccharomyces Genome Database Genes Descriptiontable sgdDescription
"Description of SGD Genes and Other Features"
    (
    string  name;        "Name in sgdGene or sgdOther table"
    string type;         "Type of feature from gff3 file"
    lstring description; "Description of feature"
    )
Saccharomyces Genome Database Other Featurestable sgdOther
"Features other than coding genes from yeast genome database"
    (
    string chrom;       "Chromosome in chrNN format"
    int chromStart;     "Start (zero based)"
    int chromEnd;       "End (non-inclusive)"
    string name;        "Feature name"
    int score;          "Always 0"
    char[1] strand;     "Strand: +, - or ."
    string type;        "Feature type"
    )
Sagetable sage
"Stores SAGE data in terms of UniGene identifiers"
    (
    int uni;               "Number portion of UniGene identifier"
    string gb;             "GenBank accession number"
    string gi;             "gi field in UniGene descriptions"
    lstring description;   "Description from UniGene fasta headers"
    int numTags;           "Number of tags"
    string[numTags] tags;  "Tags for this unique sequence"
    int numExps;           "Number of experiments"
    int[numExps] exps;     "Index of experiemtns in order of aves and stdevs"
    float[numExps] meds;   "Meida count of all tags for each experiment"
    float[numExps] aves;   "Average count of all tags for each experiment"
    float[numExps] stdevs  "Standard deviations of all counts for each experiment"
    )
Sage Experimentstable sageExp
"Data related to SAGE experiments, tissue descriptions, etc."
    (
    int num;               "Index of the experiment in the sage table"
    string exp;            "Experiment name"
    int totalCount;        "Sum of all the tag counts for this experiment"
    string tissueType;     "Brief description of cells used"
    string tissueDesc;     "Brief description of tissues"
    string tissueSupplier; "Who supplied the tissue"
    string organism;       "Organism source of cells"
    string organ;          "Organ identifier"
    lstring producer;      "Source of tissue"
    lstring desription;    "Description of experiment"
    )
SAM Protein Homolog Datatable protHomolog
"table to store SAM homolog results"
    (
    string  proteinID;  	"Protein ID"
    string  homologID;  	"Homolog ID"
    char[1] charin;     	"Chain"
    int     length;     	"Length of protein sequence"
    double  bestEvalue; 	"Best E-value"
    double  evalue;     	"E-value"
    string  FSSP;       	"FSSP ID"
    string  SCOPdomain; 	"SCOP domain ID"
    string  SCOPsuid;   	"SCOP sunid"
    )
SAM Data Subdirectory Linked to Known Gene IDtable samSubdir
"Link together a Known Gene ID and a gene alias"
    (
    string proteinId;   "Protein ID"
    string subdir;      "Name of the subdirectory where SAM results are"
    )
Sample Tracks for Plotting Real-valued Datatable sample9
"Describes (x,y) pairs of samples"
   {
    ushort bin;                         "A field to speed indexing added to many
                                         tables August 2001"
    string  chrom;                      "Chromosome alignment is on."
    uint    chromStart;                 "Start position in chromosome"
    uint    chromEnd;                   "End position in chromosome"
    string  name;                       "Unique index given to each block of samples"
    uint    score;                      "Overall block score from 0 to 1000 (chrN_humMusL 
					 only)"
    char[1] strand;                     "Strand: + or -"
    uint    sampleCount                 "Number of samples in this block"
    uint[sampleCount]   samplePosition  "Base position of each sample in this
                                         block, relative to chromStart"
    uint[sampleCount]   sampleHeight    "Score for each sample (y-value) from 0 to 1000"
    }
Sample Tracks for Plotting Real-valued Data (Rev 2)table wiggle
"Wiggle track values to display as y-values (first 6 fields are bed6)"
    (
    string chrom;         "Chromosome or FPC contig"
    uint chromStart;      "Start position in chromosome"
    uint chromEnd;        "End position in chromosome"
    string name;          "Name of item"
    uint span;            "Each value spans this many bases"
    uint count;           "Number of values in this block"
    uint offset;          "Offset in file to fetch data"
    string file;          "Path name to data file, one byte per value"
    double lowerLimit;    "Lowest data value in this block"
    double dataRange;     "LowerLimit + dataRange = upperLimit"
    uint validCount;      "Number of valid data values in this block"
    double sumData;       "Sum of the data points, for average and stddev calc"
    double sumSquares;    "Sum of data points squared, for stddev calc"
    )
Sanger 20 and 22 Genes - Additional Informationtable sanger22extra
"Table with additional information about a Sanger 22 gene"
    (
    string name;	  "Transcript name"
    string locus;	  "Possibly biological short name"
    lstring description;  "Description from Sanger gene GFFs"
    string geneType;	  "Type field from Sanger gene GFFs"
    string cdsType;	  "Type field from Sanger CDS GFFs"
    )
Sanger Genes (WormBase)table sangerGene
"GenePred table with proteinID field for WormBase Genes."
    (
    string name;        	"Name of gene"
    string chrom;       	"Chromosome name"
    char[1] strand;     	"+ or - for strand"
    uint txStart;       	"Transcription start position"
    uint txEnd;         	"Transcription end position"
    uint cdsStart;      	"Coding region start"
    uint cdsEnd;        	"Coding region end"
    uint exonCount;     	"Number of exons"
    uint[exonCount] exonStarts; "Exon start positions"
    uint[exonCount] exonEnds;   "Exon end positions"
    string proteinID;   	"UniProtKB protein ID"
    )
SCOP Descriptionstable scopDes
"Structural Classification of Proteins description"
    (
    int sunid;  		"Unique integer"
    char[2] type;       	"Type.  sf=superfamily, fa = family, etc."
    string sccs;        	"Dense hierarchy info."
    string sid;         	"Older ID."
    lstring description; 	"Descriptive text."
   )
Scored Reftable scoredRef
"A score, a range of positions in the genome and an extFile offset"
   (
   int bin;          	"Field used to speed indexing"  
   string chrom;      	"Chromosome (this species)"
   uint   chromStart; 	"Start position in chromosome (forward strand)"
   uint   chromEnd;   	"End position in chromosome"
   uint   extFile;	"Pointer to associated external file"
   bigint offset;	"Offset in external file"
   float score;      	"Value between 0.0 and 1.0 that loosely reflects % identity ratio. 
                      	 Derived from multiz score by dividing it by the number of pairwise 
                      	 comparisons in the multiple alignment and by the number of bases 
                      	 in the alignment."
   )
Segmental Duplicationstable genomicSuperDups
"Summary of large genomic Duplications (>1KB >90% similar)"
  (
  string chrom;       	"Chromosome or FPC contig"
  uint chromStart;   	"Start position in chromosome"
  uint chromEnd;     	"End position in chromosome"
  string name;         	"Other chromosome involved"
  uint score;        	"Score from 900-1000.  1000 is best"
  char[1] strand;       "Value should be + or -"
  string otherChrom;   	"Other chromosome or FPC contig"
  uint otherStart;   	"Start in other  sequence"
  uint otherEnd;     	"End in other  sequence"
  uint otherSize;    	"Total size of other sequence"
  uint uid;       	"Unique ID"
  uint posBasesHit;     "HitPositive UnCovered"
  string testResult;    "HitPositive (yes or no) UnCovered (covered=0)"
  string verdict;       "Real or Allele"
  string alignfile;     "Alignment file path"
  uint alignL;      	"Spaces/positions in alignment"
  uint indelN;       	"Number of indels"
  uint indelS;      	"Indel spaces"
  uint alignB;       	"Bases Aligned"
  uint matchB;      	"Aligned bases that match"
  uint mismatchB;    	"Aligned bases that do not match"
  uint transitionsB;    "Number of transitions"
  uint transversionsB;  "Number of transversions"
  float fracMatch;    	"Fraction of matching bases"
  float fracMatchIndel; "Fraction of matching bases with indels"
  float jcK;          	"K-value calculated with Jukes-Cantor"
  float k2K;          	"Kimura K"
  )
 Seqtable seq
"Locations of database table sequences referenced in external fasta files"
   (
   int id; 		  "Sequence ID"
   string acc; 		  "Accession or name of sequence"
   int size;		  "Size of sequence"
   date gb_date;	  "Modification date for genbank mRNAs/ESTs"
   int extFile;		  "ID of file in extFile table"
   int file_offset;	  "Byte offset of sequence start in fasta file"
   int file_size;	  "Size of sequence record in fasta file (includes fasta 
			   sequence header"
   )                                                                           
 Simple RepeatsThis table was generated by the trf program.  It does a more thorough job 
of finding simple tandem repeats than RepeatMasker does.table simpleRepeat
"Describes the Simple Tandem Repeats"
   (
   ushort  bin;           "A field to speed indexing"
   uint    matches;       "Number of bases that match that aren't repeats"
   uint    misMatches;    "Number of bases that don't match"
   string chrom;          "Chromosome or FPC contig"
   uint   chromStart;     "Start position in chromosome"
   uint   chromEnd;       "End position in chromosome"
   string name;           "Simple Repeats tag name"
   uint   period;         "Length of repeat unit"
   float  copyNum;        "Mean number of copies of repeat"
   uint   consensusSize;  "Length of consensus sequence"
   uint   perMatch;       "Percentage Match"
   uint   perIndel;       "Percentage Indel"
   uint   score;          "Score between  and .  Best is ."
   uint   A;              "Number of A's in repeat unit"
   uint   C;              "Number of C's in repeat unit"
   uint   G;              "Number of G's in repeat unit"
   uint   T;              "Number of T's in repeat unit"
   float  entropy;        "Entropy"
   string sequence;       "Sequence of repeat unit element"
   )
 SNP Map (combined table of SNPs, hg17 and later)table snp
"Polymorphism data from dbSnp XML files or genotyping arrays"
    (
    string  chrom;      "Chromosome"
    uint    chromStart; "Start position in chrom"
    uint    chromEnd;   "End position in chrom"
    string  name;       "Reference SNP identifier or Affy SNP name"
    uint    score;      "Not used"
    char[1] strand;     "Which DNA strand contains the observed alleles"
    string  observed;   "The sequences of the observed alleles"
    string  molType;    "Sample type from exemplar ss"
    string  class;      "The class of variant"
    string  valid;      "The validation status of the SNP"
    float   avHet;      "The average heterozygosity from all observations"
    float   avHetSE;    "The Standard Error for the average heterozygosity"
    string  func;       "The functional category of the SNP"
    string  locType;    "How the variant affects the reference sequence"
    string  source;     "Source of the data - dbSnp, Affymetrix, ..."
    string  exception;  "List of exceptionIds for 'invariant' conditions"
    )
SNP Exceptionstable snpExceptions
"Set of queries to look for snps that appear problematic"
    (
    uint    exceptionId; "Unique ID for this exception"
    string  query;       "SQL string to retrieve bad records"
    uint    num;         "Count of SNPs that fail this condition"
    string  description; "Text string for readability"
    string  resultPath;  "Path for results file"
    )
SNP Map (combined table of SNPs, hg13-hg16)table snpMap
"SNP positions from various sources"
    (
    string chrom;       "Chromosome or 'unknown'"
    uint   chromStart;  "Start position in chrom"
    uint   chromEnd;    "End position in chrom"
    string name;        "Name of SNP - rsId or Affy name"
    string source;      "BAC_OVERLAP | MIXED | RANDOM | OTHER | Affy10K | Affy120K
"
    string type;        "SNP | INDEL | SEGMENTAL"
    )
Softberry Genes - Protein Homologiestable softberryHom
"Protein homologies behind Softberry genes"
    (
    string name;          "Softberry gene name"
    string giString;      "String with GenBank gi and accession"
    lstring description;  "Freeform (except for no tabs) description"
    )
Standard Linked FeaturesThe phMouse and genscanSubopt tables use the first 7 fields of this table.
The bacEndPairs table uses all fields.table lfs
"Standard linked features series table"
   (
   short  bin;                  "Bin number for browser speedup"
   string chrom;                "Chromosome or FPC contig"
   uint   chromStart;           "Start position of clone in chromosome"
   uint   chromEnd;             "End position of clone in chromosome"
   string name;                 "Name of clone"
   uint   score;                "Score = 1000/(# of times clone appears in assembly)"
   char[1] strand;              "Value should be + or -"
   string pslTable;             "Table which contains corresponding PSL records for 
				 linked features"
   uint   lfCount;              "Number of linked features in the series"
   uint[lfCount]   lfStarts;    "Comma-separated list of start positions of each linked 
				 feature in genomic"
   uint[lfCount]   lfSizes;     "Comma-separated list of sizes of each linked feature 
				 in genomic"
   string[lfCount] lfNames;     "Comma-separated list of names of linked features"
   )
 STS and FISH Clone Positions(obsolete as of Apr. 2001, replaced by stsMap)table stsMarker  
"STS marker and its position on golden path and various maps"
    ( 
    string chrom;            "Chromosome or 'unknown'"
    int    chromStart;       "Start position in chrom (-1 if unpositioned)"
    uint   chromEnd;         "End position in chrom" 
    string name;             "Name of STS marker"  
    uint   score;            "Score of a marker - depends on how many contigs it hits"  
    uint   identNo;          "Identification number of STS" 
    string ctgAcc;           "Contig accession number
    string otherAcc;         "Accession number of other contigs that the marker hits"  
    string genethonChrom;    "Chromosome from Genethon map or 0 if none" 
    float  genethonPos;      "Position on Genethon map"
    string marshfieldChrom;  "Chromosome from Marshfield map or 0 if none"
    float  marshfieldPos;    "Position on Marshfield map" 
    string gm99Gb4Chrom;     "Chromosome from GeneMap99 map or 0 if none"
    float  gm99Gb4Pos;       "Position on GeneMap99 map" 
    string shgcG3Chrom;      "Chromosome from G3 map or 0 if none"
    float  shgcG3Pos;        "Position on G3 map" 
    string wiYacChrom;       "Chromosome from Whitehead YAC map or 0 if none"
    float  wiYacPos;         "Position on Whitehead YAC map" 
    string shgcTngChrom;     "Chromosome from TNG map or 0 if none" 
    float  shgcTngPos;       "Position on TNG map" 
    string fishChrom;        "Chromosome from FISH map or 0 if none" 
    string beginBand;        "Beginning of range of bands on FISH map"
    string endBand;          "End of range of bands on FISH map"
    string lab;              "Laboratory that placed the FISH clone"
    )             
STS Clone Positionstable stsMap
"STS marker and its position on golden path and various maps"
    (
    string chrom;	        "Chromosome or 'unknown'"
    int chromStart;             "Start position in chrom - negative 1 if unpositioned"
    uint chromEnd;        	"End position in chrom"
    string name;	        "Name of STS marker"
    uint score;	                "Score of a marker = 1000/(# of placements)"
    uint identNo;        	"Identification number of STS"
    string ctgAcc;	        "Contig accession number"
    string otherAcc;	        "Accession number of other contigs that the marker hits"
    string genethonChrom;	"Chromosome (no chr) from Genethon map or 0 if none"
    float genethonPos;		"Position on Genethon map"
    string marshfieldChrom;	"Chromosome (no chr) from Marshfield map or 0 if none"
    float marshfieldPos;	"Position on Marshfield map"
    string gm99Gb4Chrom;	"Chromosome (no chr) from GeneMap99 map or 0 if none"
    float gm99Gb4Pos;		"Position on gm99_bg4 map"
    string shgcTngChrom;	"Chromosome (no chr) from shgc_tng map or 0 if none"
    float shgcTngPos;		"Position on shgc_tng map"
    string shgcG3Chrom;		"Chromosome (no chr) from Stanford G3 map or 0 if none"
    float shgcG3Pos;		"Position on shgc_g3 map"
    string wiYacChrom;		"Chromosome (no chr) from Whitehead YAC map or 0 if none"
    float wiYacPos;		"Position on wi_yac map"
    string wiRhChrom;		"Chromosome (no chr) from Whitehead RH map or 0 if none"
    float wiRhPos;		"Position on wi_rh map"
    string fishChrom;		"Chromosome (no chr) from FISH map or 0 if none"
    string beginBand;		"Beginning of range of bands on FISH map"
    string endBand;		"End of range of bands on FISH map"
    string lab;			"Laboratory that placed the FISH clone"
    )
STS Clone Positions (MGI)table stsMapMouse
"STS marker and its position on mouse assembly"
    (
    string chrom;       "Chromosome or 'unknown'"
    int chromStart;     "Start position in chromosome (-1 if unpositioned)"
    uint chromEnd;      "End position in chromosome"
    string name;        "Name of STS marker"
    uint score;         "Score of a marker = 1000/(# of placements)"
    uint identNo;       "UCSC ID number"
    uint probeId;       "Probe identification number of STS"
    uint markerId;      "Marker identification number of STS"
    )
STS Clone Positions (NCBI)table stsMapMouseNew
"STS marker and its position on mouse assembly - mm3 and higher"
    (
    string chrom;       "Chromosome or 'unknown'"
    int chromStart;     "Start position in chromosome (-1 if unpositioned)"
    uint chromEnd;      "End position in chromosome"
    string name;        "Name of STS marker"
    uint score;         "Score of a marker = 1000/(# of placements)"
    uint identNo;       "Identification number of STS"
    string ctgAcc;      "Contig accession number"
    string otherAcc;    "Accession number of other contigs that the marker hits"
    string rhChrom;     "Chromosome (no chr) from RH map or 0 if none"
    float rhPos;        "Position on RH map"
    float rhLod;        "LOD score of RH map"
    string fhhChr;      "Chromosome (no chr) from FHHxACI genetic or 0 if none"
    float fhhPos;       "Position on FHHxACI map"
    string shrspChrom;  "Chromosome (no chr) from SHRSPxBN geneticmap or 0 if none"
    float shrspPos;     "Position on SHRSPxBN genetic map"
    )
STS Clone Positions (Rat)table stsMapRat
"STS marker and its position on rat assembly"
    (
    string chrom;       "Chromosome or 'unknown'"
    int chromStart;     "Start position in chromosome (-1 if unpositioned)"
    uint chromEnd;      "End position in chromosome"
    string name;        "Name of STS marker"
    uint score;         "Score of a marker = 1000/(# of placements)"
    uint identNo;       "Identification number of STS"
    string ctgAcc;      "Contig accession number"
    string otherAcc;    "Accession number of other contigs that the marker hits"
    string rhChrom;     "Chromosome (no chr) from RH map or 0 if none"
    float rhPos;        "Position on RH map"
    float rhLod;        "LOD score of RH map"
    string fhhChr;      "Chromosome (no chr) from FHHxACI genetic or 0 if none"
    float fhhPos;       "Position on FHHxACI map"
    string shrspChrom;  "Chromosome (no chr) from SHRSPxBN geneticmap or 0 if none"
    float shrspPos;     "Position on SHRSPxBN genetic map"
    )
STS Marker Aliases and Associated Identification Numberstable stsAlias
"STS marker aliases and associated identification numbers"
    (
    string alias;       "STS marker name"
    uint identNo;       "Identification number of STS marker"
    string trueName;    "Official UCSC name for marker"
    )
STS Marker Constant Informationtable stsInfo
"Constant STS marker information"
    (
    uint identNo;                 "UCSC identification number"
    string name;                  "Official UCSC name"
    uint gbCount;                 "Number of related GenBank accessions"
    string[gbCount] genbank;      "Related GeneBank accessions"
    uint gdbCount;                "Number of related GDB identifiers"
    string[gdbCount] gdb;         "Related GDB identifiers"
    uint nameCount;               "Number of alias names"
    string[nameCount] otherNames; "Alias names"
    uint dbSTSid;                 "ID number in UniSTS or dbSTS"
    uint otherDbstsCount;         "Number of related dbSTS IDs"
    uint[otherDbstsCount] otherDbSTS;  "Related dbSTS IDs"
    string leftPrimer;            "5' primer sequence"
    string rightPrimer;           "3' primer sequence"
    string distance;              "Length of STS sequence"
    string organism;              "Organism for which STS discovered"
    uint sequence;                "Whether the full sequence is available (1) or not
				   (0) for STS"
    uint otherUCSCcount;          "Number of related active UCSC ids"
    uint[otherUCSCcount] otherUCSC;  "Related active UCSC ids"
    uint mergeUCSCcount;          "Number of merged inactive UCSC ids"
    uint[mergeUCSCcount] mergeUCSC;  "Related merged inactive UCSC ids"
    string genethonName;          "Name in Genethon map"
    string genethonChr;           "Chromosome in Genethon map"
    float genethonPos;            "Position in Genethon map"
    float genethonLOD;            "LOD score in Genethon map"
    string marshfieldName;        "Name in Marshfield map"
    string marshfieldChr;         "Chromosome in Marshfield map"
    float marshfieldPos;          "Position in Marshfield map"
    float marshfieldLOD;          "LOD score in Marshfield map"
    string wiyacName;             "Name in WI YAC map"
    string wiyacChr;              "Chromosome in WI YAC map"
    float wiyacPos;               "Position in WI YAC map"
    float wiyacLOD;               "LOD score in WI YAC map"
    string wirhName;              "Name in WI RH map"
    string wirhChr;               "Chromosome in WI RH map"
    float wirhPos;                "Position in WI RH map"
    float wirhLOD;                "LOD score in WI RH map"
    string gm99gb4Name;           "Name in GeneMap99 GB4 map"
    string gm99gb4Chr;            "Chromosome in GeneMap99 GB4 map"
    float gm99gb4Pos;             "Position in GeneMap99 GB4 map"
    float gm99gb4LOD;             "LOD score in GeneMap99 GB4 map"
    string gm99g3Name;            "Name in GeneMap99 G3 map"
    string gm99g3Chr;             "Chromosome in GeneMap99 G3 map"
    float gm99g3Pos;              "Position in GeneMap99 G3 map"
    float gm99g3LOD;              "LOD score in GenMap99 G3 map"
    string tngName;               "Name in Stanford TNG map"
    string tngChr;                "Chromosome in Stanford TNG map"
    float tngPos;                 "Position in Stanford TNG map"
    float tngLOD;                 "LOD score in Stanford TNG map"
    )
STS Marker Constant Information (Revised version)table stsInfo2
"Constant STS marker information - revision"
    (
    uint identNo;                 "UCSC identification number"
    string name;                  "Official UCSC name"
    uint gbCount;                 "Number of related GenBank accessions"
    string[gbCount] genbank;      "Related GeneBank accessions"
    uint gdbCount;                "Number of related GDB identifiers"
    string[gdbCount] gdb;         "Related GDB identifies"
    uint nameCount;               "Number of alias names"
    string[nameCount] otherNames; "Alias names"
    uint dbSTSid;                 "ID number in UniSTS or dbSTS"
    uint otherDbstsCount;         "Number of related dbSTS IDs"
    uint[otherDbstsCount] otherDbSTS;  "Related dbSTS IDs"
    string leftPrimer;            "5' primer sequence"
    string rightPrimer;           "3' primer sequence"
    string distance;              "Length of STS sequence"
    string organism;              "Organism for which STS discovered"
    uint sequence;                "Whether the full sequence is available (1) or not 
				   (0) for STS"
    uint otherUCSCcount;          "Number of related active UCSC ids"
    uint[otherUCSCcount] otherUCSC;  "Related active UCSC ids"
    uint mergeUCSCcount;          "Number of merged inactive UCSC ids"
    uint[mergeUCSCcount] mergeUCSC;  "Related merged inactive UCSC ids"
    string genethonName;          "Name in Genethon map"
    string genethonChr;           "Chromosome in Genethon map"
    float genethonPos;            "Position in Genethon map"
    float genethonLOD;            "LOD score in Genethon map"
    string marshfieldName;        "Name in Marshfield map"
    string marshfieldChr;         "Chromosome in Marshfield map"
    float marshfieldPos;          "Position in Marshfield map"
    float marshfieldLOD;          "LOD score in Marshfield map"
    string wiyacName;             "Name in WI YAC map"
    string wiyacChr;              "Chromosome in WI YAC map"
    float wiyacPos;               "Position in WI YAC map"
    float wiyacLOD;               "LOD score in WI YAC map"
    string wirhName;              "Name in WI RH map"
    string wirhChr;               "Chromosome in WI RH map"
    float wirhPos;                "Position in WI RH map"
    float wirhLOD;                "LOD score in WI RH map"
    string gm99gb4Name;           "Name in GeneMap99 GB4 map"
    string gm99gb4Chr;            "Chromosome in GeneMap99 GB4 map"
    float gm99gb4Pos;             "Position in GeneMap99 GB4 map"
    float gm99g3LOD;              "LOD score in GenMap99 G3 map"
    string tngName;               "Name in Stanford TNG map"
    string tngChr;                "Chromosome in Stanford TNG map"
    float tngPos;                 "Position in Stanford TNG map"
    float tngLOD;                 "LOD score in Stanford TNG map"
    string decodeName;            "Name in deCODE map"
    string decodeChr;             "Chromosome in deCODE TNG map"
    float decodePos;              "Position in deCODE TNG map"
    float decodeLOD;              "LOD score in deCODE TNG map"
    )
STS Marker Constant Information (Mouse - mm1, mm2)table stsInfoMouse
"Constant STS marker information for the mouse genome"
    (
    uint identNo;                "UCSC identification number"
    string name;                 "Official UCSC name"
    uint MGIPrimerID;            "STS primer's MGI ID, or 0 if N/A"
    string primerName;           "STS primer's name"
    string primerSymbol;         "STS primer's symbol"
    string primer1;              "Primer1 sequence"
    string primer2;              "Primer2 sequence"
    string distance;             "Length of STS sequence"
    uint sequence;               "Whether full sequence is available (1) 
                                     or not (0) for STS"
    uint MGIMarkerID;            "STS marker's MGI ID, or 0 if N/A"
    string stsMarkerSymbol;      "Symbol of STS marker"
    string Chr;                  "Chromosome in genetic map"
    float geneticPos;            "Position in genetic map 
                                     (-2 if N/A, -1 if syntenic)"
    string stsMarkerName;        "Name of STS Marker"
    uint LocusLinkID;            "Locuslink ID, or 0 if N/A"
    )
STS Marker Constant Information (Mouse - mm3 and higher)table stsInfoMouseNew
"Constant STS marker information for the mouse genome - mm3 and higher"
    (
    uint identNo;                "UCSC identification number"
    string name;                 "Official UCSC name"
    uint RGDId;		   	 "Marker's RGD ID"
    string RGDName;		 "Marker's RGD name"	
    uint UiStsId;		 "Marker's UiStsId"	   
    uint nameCount;		 "Number of alias"
    string alias;		 "Alias, or N/A"
    
    string primer1;          	 "Primer1 sequence"
    string primer2;          	 "Primer2 sequence"
    string distance;             "Length of STS sequence"
    uint sequence;               "Whether the full sequence is available (1) or not 
				  (0) for STS"
    string organis; 		 "Organism for which STS discovered"
   
    string fhhName;	         "WI_Mouse_Genetic map"
    string fhhChr;               "Chromosome in Genetic map"
    float fhhGeneticPos;         "Position in Genetic map"
    
    string shrspName;	         "MGD map"
    string shrspChr;             "Chromosome in Genetic map"
    float shrspGeneticPos;       "Position in Genetic map"
    string rhName;	    	 "MRC_RH map"
    string rhChr;                "Chromosome in Genetic map"
    float rhGeneticPos;          "Position in Genetic map"
    float RHLOD;		 "LOD score of RH map"
    string GeneName;             "Associated gene name"
    string GeneID;               "Associated gene ID"
    string clone;		 "Clone sequence"
    )
STS Marker Constant Information (Rat)table stsInfoRat
"Constant STS marker information for the rat genome"
    (
    uint identNo;                "UCSC identification number"
    string name;                 "Official UCSC name"
    uint RGDId;		   	 "Marker's RGD ID"
    string RGDName;		 "Marker's RGD name"	
    uint UiStsId;		 "Marker's UiStsId"	   
    uint nameCount;		 "Number of alias"
    string alias;		 "Alias, or N/A"
    
    string primer1;          	 "Primer1 sequence"
    string primer2;          	 "Primer2 sequence"
    string distance;             "Length of STS sequence"
    uint sequence;               "Whether the full sequence is available (1) or not 
				  (0) for STS"
    string organis; 		 "Organism for which STS discovered"
   
    string fhhName;	         "WI_Mouse_Genetic map"
    string fhhChr;               "Chromosome in Genetic map"
    float fhhGeneticPos;         "Position in Genetic map"
    
    string shrspName;	         "MGD map"
    string shrspChr;             "Chromosome in Genetic map"
    float shrspGeneticPos;       "Position in Genetic map"
    string rhName;	    	 "MRC_RH map"
    string rhChr;                "Chromosome in Genetic map"
    float rhGeneticPos;          "Position in Genetic map"
    float RHLOD;		 "LOD score of RH map"
    string GeneName;             "Associated gene name"
    string GeneID;               "Associated gene ID"
    string clone;		 "Clone sequence"
    )
Superfamily Assignmentstable sfAssign
"Superfamily assignment table"
  (
  string genomeID;      "Genome ID"
  string seqID;         "Sequence ID"
  string modelID;       "Model ID"
  string region;        "Region"
  string eValue;        "E value"
  string sfID;          "Superfamily entry ID"
  string sfDesc;        "Superfamily entry description"
  )
 Superfamily Descriptiontable sfDes 
"Superfamily description table"
  (
  int id;                       "ID"
  char[2] level;                "Level"
  string classification;        "Classification"
  string name;                  "Name"
  string description;           "Description"
  )
 Superfamily Summary Entry Descriptiontable sfDescription
"Stores domain descriptions for the Superfamily track"
   (
    string name; 	     "Superfamily ID (same as Ensembl transcript name)"
    string proteinID; 	     "ID of corresponding Ensembl translation"
    string description;	     "Domain description"
   )                                                                           
UniProtKB IDs Linked to Disease Descriptionstable spDisease
"A cross-reference table between UniProtKB IDs and disease description."
   (
   string accession;       "UniProtKB accession number"
   string displayID;       "UniProtKB display ID"
   lstring diseaseDesc;    "Disease description"
   )
 UniProtKB IDs Linked to InterPro IDstable swInterPro
"A cross-reference table between UniProtKB accession IDs and InterPro IDs."
        (
        string accession;       "UniProtKB accession number"
        string  interProId;      "InterPro ID"
        )
UniProtKB IDs Linked to Organismstable spOrganism 
"A cross-reference table between UniProtKB display IDs and taxonomy numbers."
   (
   string displayID;       "UniProtKB display ID"
   string organism;        "Taxonomy number"
   )
 UniProtKB IDs Linked to Other Databasestable spXref2
"A xref table between UniProtKB ids and other databases."
   (
   string accession;       "UniProtKB accession number"
   string displayID;       "UniProtKB display ID"
   string division;        "UniProtKB division"
   int    bioentryID;      "Biosql bioentry ID"
   int    biodatabaseID;   "Biosql biodatabase ID"
   string description;     "Description"
   string hugoSymbol;      "HUGO Gene Nomenclature Committee gene symbol"
   string hugoDesc;        "HUGO Gene Nomenclature Committee gene description"
   )
 UniProtKB IDs Linked to Secondary IDstable spSecondaryID 
"A cross-reference table between UniProtKB accession IDs and secondary accessions."
   (
   string displayID;       "UniProtKB display ID"
   string accession;       "UniProtKB accession number"
   string accession2;      "UniProtKB secondary accession number"
   )
 UniProtKB mRNAtable spMrna
"Associates UniProtKB IDs with mRNA IDs"
    (
    string spID; 	"UniProtKB ID"
    string mrnaID;	"mRNA ID"
    )
UniProtKB PSI-BLAST E-valuetable spPsiBlast
"PSI-BLAST all-against-all of UniProtKB proteins. UniProtKB accessions 
are mapped to Known Genes IDs before being loaded into the table."
    (
    string kgId1;       "Known Gene ID of one protein"
    string kgId2;       "Known Gene ID of other protein"
    float eValue;       "Best bi-directional E-value"
    )
tBLASTn Protein Track Mappingstable blastRef
"Mapping table for tblastn protein tracks"
    (
    string acc;         "Accession"
    string geneId;      "Gene name"
    string refPos;      "Reference position"
    string extra1;      "Other link 1 (e.g. UniProtKB name)
    string extra2;      "Other link 2"
    )
Tiling Path of Clones through a Chromosometable tilingPath
"A tiling path of clones through a chromosome"
    (
    string chrom;	"Chromosome name: chr1, chr2, etc."
    string accession;   "Clone accession or ? or GAP"
    string clone;       "Clone name in BAC library"
    string contig;      "Contig (or gap size)"
    int chromIx;        "Number of clone in tiling path starting chrom start"
    )
Transcription Factor Binding Motif (HarbisonGordon et al.)table transRegCodeMotif
"A transcription factor binding motif according to Harbison Gordon et al"    
    (
    string name;                        "Motif name."
    int columnCount;                    "Count of columns in motif."
    float[columnCount] aProb;           "Probability of A's in each column."
    float[columnCount] cProb;           "Probability of C's in each column."
    float[columnCount] gProb;           "Probability of G's in each column."
    float[columnCount] tProb;           "Probability of T's in each column."
    )
Transcription Factor Binding Sitestable tfbsCons
"TFBS data"
    (
    string chrom;      	"Chromosome"
    uint   chromStart; 	"Start position in chromosome"
    uint   chromEnd;   	"End position in chromosome"
    string name;       	"Name of item"
    uint   score;      	"Score from 0-1000"
    char[1] strand;    	"+ or -"
    char[6] species;  	"Common name, scientific name"
    char[64] factor;  	"Factor"
    char[10] id;  	"ID"
    )
Transcription Factor Binding Sites and CHIP/CHIP Probe Infotable transRegCodeProbe
"CHIP/CHIP Probe and Transcription Factor Binding Info"    
    (
    string chrom;       	"Chromosome binding site is on"
    uint chromStart;    	"Start position in chromosome"
    uint chromEnd;      	"End position in chromosome" 
    string name;        	"Name of probe" 
    uint tfCount;       	"Count of bound transcription factors_conditions"
    string[tfCount] tfList;    	"List of bound transcription factors_conditions
"   
    float[tfCount] bindVals;   	"E-values for factor binding (lower is better)"
    )
Transcription Factor Binding Sites - CHIP/CHIP Experimentstable transRegCode
"Transcription factor binding sites from CHIP/CHIP experiments and conservation"
    (
    string chrom;       	"Chromosome binding site is on"
    uint chromStart;    	"Start position in chromosome"
    uint chromEnd;      	"End position in chromosome"
    string name;        	"Name of transcription factor"
    uint score;         	"Score from 0 to 1000"
    string chipEvidence; 	"Evidence strength from CHIP/CHIP assay"
    uint consSpecies;   	"Number of species conserved in"
    )
Transcription Factor Binding Sites Conservation Map Datatable tfbsConsMap
"tfbsConsMap Data"
    (
    string id;   "TRANSFAC id"
    string ac;   "gene-regulation.com AC"
    )
Transcription Factor Growth Conditiontable transRegCodeCondition
"Growth condition associated with a transcription factor"
    (
    string name;  "Name of transcription factor"
    string growthCondition; "Growth condition seen in"
    )
Vega Infotable vegaInfo
"Vega Genes track additional information"
    (
    string transcriptId;        "Vega transcript ID"
    string otterId;             "Otter (Ensembl db) transcript ID"
    string geneId;              "Vega gene ID"
    string method;              "GTF method field"
    string geneDesc;            "Vega gene description"
    )
Waba Alignments (Abbreviated version)table chrN_wabaCbr
"Abbreviated Waba alignment table for quick display"
    (
    string query;	"Name of foreign sequence"
    uint chromStart;	"Start in genomic sequence"
    uint chromEnd; 	"End in genomic sequence"
    char strand; 	"Relative orientation"
    uint milliScore; 	"Identity in parts per thousand"
    longblob squeezed;	"HMM symbols with target inserts squeezed out"
    }
Waba Alignments (Full description)table wabaCbr
"Information on a Waba alignment"
  (
  string query; 	"Name of foreign sequence"
  uint qStart;		"Start of alignment in query"
  uint qEnd; 		"End of alignment in query"
  char qStrand;		"Which strand"
  string chrom; 	"Which chromosome"
  uint chromStart;	"Start in chromosome sequence"
  uint chromEnd; 	"End in chromosome sequence"
  uint milliScore	"Identity in parts per thousand"
  uint symCount;	"Number of symbols in following blobs"
  longblob qSym; 	"Query sequence and insert chars"
  longblob tSym;	"Target sequence and insert chars"
  longblob hSym;	"HMM symbols"
  )
 
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