blastHg16KG table psl\ "Summary info about a patSpace alignment"\ (\ 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 strand. First character query, second target (optional)"\ 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"\ 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."\ )\ PslInfo chainCi1 table 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 chainCi1Link table chainGap\ "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"\ )\ chromInfo table chromInfo\ "Chromosome names and sizes"\ (\ string chrom;\ "Reference sequence chromosome or scaffold"\ uint size; "Chromosome size"\ string fileName; "Chromosome file (raw one byte per base)"\ )\ ChromInfo extFile table extFile\ "External (i.e. not in database) data file info"\ (\ uint id;\ \ "ID/index"\ string name;\ "File name (without path)"\ string path;\ "Full path of file"\ long size;\ \ "byte size of file"\ )\ extFileInfo gap table agpGap\ "Gaps in golden path"\ (\ string chrom;\ "Reference sequence chromosome or scaffold"\ 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."\ )\ BED gcPercent table gcPercent\ "Displays GC percentage in 20Kb blocks for genome"\ (\ string chrom; "Reference sequence chromosome or scaffold"\ uint chromStart; "Start position in genoSeq"\ uint chromEnd; "End position in genoSeq"\ string name; "Constant string GCpct"\ uint gcPpt; "GC percentage for 20Kb block"\ )\ GCpercent grp table grp\ "This describes a group of annotation tracks."\ (\ string name; "Group name. Connects with trackDb.grp"\ string label; "Label to display to user"\ float priority; "0 is top"\ )\ TrackGroups hgFindSpec table hgFindSpec\ "This 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."\ )\ HgFindSpec history table history\ "Who loaded what tables when"\ (\ int ix;\ \ "auto_increment ID"\ uint startId;\ "First extFile index affected by this action (or 0)"\ uint endId;\ \ "Last extFile index affected by this action (or 0)"\ string who;\ \ "Unix userID that performed this action"\ string what;\ "Brief description of what table(s) were loaded"\ timestamp modTime;\ "Time of action"\ string errata;\ "Any after-the-fact comments about changes"\ )\ HistoryInfo netCi1 table 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 tandem repeats on target. -1 for undefined"\ int qTrf; "Bases of tandem repeats on query. -1 for undefined"\ )\ NetAlign netSyntenyCi1 table 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 tandem repeats on target. -1 for undefined"\ int qTrf; "Bases of tandem repeats on query. -1 for undefined"\ )\ NetAlign rmsk table rmskOut\ "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."\ )\ RepeatInfo seq table seq\ "Information about sequences contained in files described in extFile"\ (\ uint id;\ \ "ID/index"\ string acc;\ \ "Accession of sequence"\ uint size;\ \ "Size of sequence (number of bases)"\ date gb_date;\ "unused"\ uint extFile;\ "ID/index of file in extFile"\ long file_offset;\ "byte offset of sequence in file"\ uint file_size;\ "byte size of sequence in file"\ )\ seqInfo simpleRepeat table simpleRepeat\ "Describes the Simple Tandem Repeats"\ (\ string chrom; \ "Reference sequence chromosome or scaffold"\ 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; \ "Percent of A's in repeat unit"\ uint C; \ "Percent of C's in repeat unit"\ uint G; \ "Percent of G's in repeat unit"\ uint T; \ "Percent of T's in repeat unit"\ float entropy; \ "Entropy"\ lstring sequence; \ "Sequence of repeat unit element"\ )\ SimpleRepeats tableDescriptions table tableDescriptions\ "Descriptive information about database tables from autoSql / gbdDescriptions"\ (\ string tableName;\ "Name of table (with chr*_ replaced with chrN_)"\ lstring autoSqlDef;\ "Contents of autoSql (.as) table definition file"\ string gbdAnchor;\ "Anchor for table description in gbdDescriptions.html"\ )\ TableDesc trackDb table trackDb\ "This describes an annotation track."\ (\ string tableName; "Symbolic ID of Track"\ string shortLabel; "Short label displayed on left"\ string type; "Track type: bed, psl, genePred, etc."\ string longLabel; "Long label displayed in middle"\ ubyte visibility; "0=hide, 1=dense, 2=full, 3=pack, 4=squish"\ float priority; "0-100 - where to position. 0 is top"\ ubyte colorR;\ "Color red component 0-255"\ ubyte colorG;\ "Color green component 0-255"\ ubyte colorB;\ "Color blue component 0-255"\ ubyte altColorR; "Light color red component 0-255"\ ubyte altColorG; "Light color green component 0-255"\ ubyte altColorB; "Light color blue component 0-255"\ ubyte useScore; "1 if use score, 0 if not"\ ubyte private;\ "1 if only want to show it on test site"\ int restrictCount;\ "Number of chromosomes this is on (0=all though!)"\ string[restrictCount] restrictList; "List of chromosomes this is on"\ lstring url;\ "URL to link to when they click on an item"\ lstring html; "Some html to display when they click on an item"\ string grp; "Which group track belongs to"\ ubyte canPack; "1 if can pack track display, 0 otherwise"\ lstring settings; "Name/value pairs for track-specific stuff"\ )\ TrackDB