Schema for kgTargetAli

Database: hg38 Primary Table: kgTargetAli Row Count: 533,740 Data last updated: 2025-09-26
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`matches`	1288	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	0	`int(10) unsigned`	Number of bases that don't match
`repMatches`	91	`int(10) unsigned`	Number of bases that match but are part of repeats
`nCount`	0	`int(10) unsigned`	Number of 'N' bases
`qNumInsert`	0	`int(10) unsigned`	Number of inserts in query
`qBaseInsert`	0	`int(10) unsigned`	Number of bases inserted in query
`tNumInsert`	3	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	1914	`int(10) unsigned`	Number of bases inserted in target
`strand`	+	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	ENST00000832824.1	`varchar(255)`	Query sequence name
`qSize`	1379	`int(10) unsigned`	Query sequence size
`qStart`	0	`int(10) unsigned`	Alignment start position in query
`qEnd`	1379	`int(10) unsigned`	Alignment end position in query
`tName`	chr1	`varchar(255)`	Target sequence name
`tSize`	248956422	`int(10) unsigned`	Target sequence size
`tStart`	11120	`int(10) unsigned`	Alignment start position in target
`tEnd`	14413	`int(10) unsigned`	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	91,218,109,961,	`longblob`	Size of each block
`qStarts`	0,91,309,418,	`longblob`	Start of each block in query.
`tStarts`	11120,12009,12612,13452,	`longblob`	Start of each block in target.

Connected Tables and Joining Fields


	hg38.bioCycPathway.kgID (via kgTargetAli.qName) hg38.ccdsKgMap.geneId (via kgTargetAli.qName) hg38.ceBlastTab.query (via kgTargetAli.qName) hg38.dmBlastTab.query (via kgTargetAli.qName) hg38.drBlastTab.query (via kgTargetAli.qName) hg38.foldUtr3.name (via kgTargetAli.qName) hg38.foldUtr5.name (via kgTargetAli.qName) hg38.gnfAtlas2Distance.query (via kgTargetAli.qName) hg38.gnfAtlas2Distance.target (via kgTargetAli.qName) hg38.gnfU95Distance.query (via kgTargetAli.qName) hg38.gnfU95Distance.target (via kgTargetAli.qName) hg38.humanHprdP2P.query (via kgTargetAli.qName) hg38.humanHprdP2P.target (via kgTargetAli.qName) hg38.humanVidalP2P.query (via kgTargetAli.qName) hg38.humanVidalP2P.target (via kgTargetAli.qName) hg38.humanWankerP2P.query (via kgTargetAli.qName) hg38.humanWankerP2P.target (via kgTargetAli.qName) hg38.keggPathway.kgID (via kgTargetAli.qName) hg38.kgAlias.kgID (via kgTargetAli.qName) hg38.kgColor.kgID (via kgTargetAli.qName) hg38.kgProtAlias.kgID (via kgTargetAli.qName) hg38.kgSpAlias.kgID (via kgTargetAli.qName) hg38.kgXref.kgID (via kgTargetAli.qName) hg38.knownAttrs.kgID (via kgTargetAli.qName) hg38.knownBlastTab.query (via kgTargetAli.qName) hg38.knownBlastTab.target (via kgTargetAli.qName) hg38.knownCanonical.transcript (via kgTargetAli.qName) hg38.knownCds.name (via kgTargetAli.qName) hg38.knownGene.name (via kgTargetAli.qName) hg38.knownGeneMrna.name (via kgTargetAli.qName) hg38.knownGenePep.name (via kgTargetAli.qName) hg38.knownIsoforms.transcript (via kgTargetAli.qName) hg38.knownToEnsembl.name (via kgTargetAli.qName) hg38.knownToGnfAtlas2.name (via kgTargetAli.qName) hg38.knownToHprd.name (via kgTargetAli.qName) hg38.knownToKeggEntrez.name (via kgTargetAli.qName) hg38.knownToLocusLink.name (via kgTargetAli.qName) hg38.knownToLynx.name (via kgTargetAli.qName) hg38.knownToMrna.name (via kgTargetAli.qName) hg38.knownToMrnaSingle.name (via kgTargetAli.qName) hg38.knownToMupit.name (via kgTargetAli.qName) hg38.knownToNextProt.name (via kgTargetAli.qName) hg38.knownToPfam.name (via kgTargetAli.qName) hg38.knownToRefSeq.name (via kgTargetAli.qName) hg38.knownToSuper.gene (via kgTargetAli.qName) hg38.knownToTag.name (via kgTargetAli.qName) hg38.knownToU133.name (via kgTargetAli.qName) hg38.knownToU95.name (via kgTargetAli.qName) hg38.knownToVisiGene.name (via kgTargetAli.qName) hg38.knownToWikipedia.name (via kgTargetAli.qName) hg38.mmBlastTab.query (via kgTargetAli.qName) hg38.rnBlastTab.query (via kgTargetAli.qName) hg38.scBlastTab.query (via kgTargetAli.qName) hg38.ucscScop.ucscId (via kgTargetAli.qName) knownGeneV39.bioCycPathway.kgID (via kgTargetAli.qName) knownGeneV39.ceBlastTab.query (via kgTargetAli.qName) knownGeneV39.dmBlastTab.query (via kgTargetAli.qName) knownGeneV39.drBlastTab.query (via kgTargetAli.qName) knownGeneV39.foldUtr3.name (via kgTargetAli.qName) knownGeneV39.foldUtr5.name (via kgTargetAli.qName) knownGeneV39.gnfAtlas2Distance.query (via kgTargetAli.qName) knownGeneV39.gnfAtlas2Distance.target (via kgTargetAli.qName) knownGeneV39.kgAlias.kgID (via kgTargetAli.qName) knownGeneV39.kgColor.kgID (via kgTargetAli.qName) knownGeneV39.kgProtAlias.kgID (via kgTargetAli.qName) knownGeneV39.kgSpAlias.kgID (via kgTargetAli.qName) knownGeneV39.kgTargetAli.qName (via kgTargetAli.qName) knownGeneV39.kgXref.kgID (via kgTargetAli.qName) knownGeneV39.knownAttrs.kgID (via kgTargetAli.qName) knownGeneV39.knownBlastTab.query (via kgTargetAli.qName) knownGeneV39.knownBlastTab.target (via kgTargetAli.qName) knownGeneV39.knownCanonical.protein (via kgTargetAli.qName) knownGeneV39.knownCanonical.transcript (via kgTargetAli.qName) knownGeneV39.knownCds.name (via kgTargetAli.qName) knownGeneV39.knownGene.name (via kgTargetAli.qName) knownGeneV39.knownGeneMrna.name (via kgTargetAli.qName) knownGeneV39.knownGenePep.name (via kgTargetAli.qName) knownGeneV39.knownIsoforms.transcript (via kgTargetAli.qName) knownGeneV39.knownToEnsembl.name (via kgTargetAli.qName) knownGeneV39.knownToGnfAtlas2.name (via kgTargetAli.qName) knownGeneV39.knownToHprd.name (via kgTargetAli.qName) knownGeneV39.knownToLocusLink.name (via kgTargetAli.qName) knownGeneV39.knownToMrna.name (via kgTargetAli.qName) knownGeneV39.knownToMrnaSingle.name (via kgTargetAli.qName) knownGeneV39.knownToMupit.name (via kgTargetAli.qName) knownGeneV39.knownToPfam.name (via kgTargetAli.qName) knownGeneV39.knownToRefSeq.name (via kgTargetAli.qName) knownGeneV39.knownToSuper.gene (via kgTargetAli.qName) knownGeneV39.knownToTag.name (via kgTargetAli.qName) knownGeneV39.knownToU133.name (via kgTargetAli.qName) knownGeneV39.knownToU95.name (via kgTargetAli.qName) knownGeneV39.knownToVisiGene.name (via kgTargetAli.qName) knownGeneV39.knownToWikipedia.name (via kgTargetAli.qName) knownGeneV39.mmBlastTab.query (via kgTargetAli.qName) knownGeneV39.rnBlastTab.query (via kgTargetAli.qName) knownGeneV39.scBlastTab.query (via kgTargetAli.qName) knownGeneV39.ucscScop.ucscId (via kgTargetAli.qName)

Sample Rows

bin	matches	repMatches	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	1288	91	3	1914	+	ENST00000832824.1	1379	1379	chr1	248956422	11120	14413	4	91,218,109,961,	0,91,309,418,	11120,12009,12612,13452,
585	1330	87	3	1864	+	ENST00000832825.1	1417	1417	chr1	248956422	11124	14405	4	87,218,109,1003,	0,87,305,414,	11124,12009,12612,13402,
585	1333	205	3	1466	+	ENST00000832826.1	1538	1538	chr1	248956422	11409	14413	4	262,218,127,931,	0,262,480,607,	11409,12009,12594,13482,
585	1315	204	3	1484	+	ENST00000832827.1	1519	1519	chr1	248956422	11410	14413	4	261,218,109,931,	0,261,479,588,	11410,12009,12612,13482,
585	1573	189	3	1222	+	ENST00000832828.1	1762	1762	chr1	248956422	11425	14409	4	246,218,109,1189,	0,246,464,573,	11425,12009,12612,13220,
585	1325	11	3	1311	+	ENST00000832829.1	1336	1336	chr1	248956422	11769	14416	4	75,218,109,934,	0,75,293,402,	11769,12009,12612,13482,
585	1260	0	3	1335	+	ENST00000832830.1	1260	1260	chr1	248956422	11818	14413	4	26,218,85,931,	0,26,244,329,	11818,12009,12612,13482,
585	1553	0	3	1031	+	ENST00000832837.1	1553	1553	chr1	248956422	11822	14406	4	22,218,127,1186,	0,22,240,367,	11822,12009,12594,13220,
585	1246	0	3	1344	+	ENST00000832833.1	1246	1246	chr1	248956422	11823	14413	4	21,218,76,931,	0,21,239,315,	11823,12009,12645,13482,
585	1275	0	3	1315	+	ENST00000832832.1	1275	1275	chr1	248956422	11823	14413	4	21,218,109,927,	0,21,239,348,	11823,12009,12612,13486,

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