Schema for xenoMrna

Database: panTro3 Primary Table: xenoMrna Row Count: 7,485,714 Data last updated: 2020-08-22
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`	31	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	1	`int(10) unsigned`	Number of bases that don't match
`repMatches`	0	`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`	0	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	0	`int(10) unsigned`	Number of bases inserted in target
`strand`	+-	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	JD469940	`varchar(255)`	Query sequence name
`qSize`	32	`int(10) unsigned`	Query sequence size
`qStart`	0	`int(10) unsigned`	Alignment start position in query
`qEnd`	32	`int(10) unsigned`	Alignment end position in query
`tName`	chr1	`varchar(255)`	Target sequence name
`tSize`	228333871	`int(10) unsigned`	Target sequence size
`tStart`	77670	`int(10) unsigned`	Alignment start position in target
`tEnd`	77702	`int(10) unsigned`	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	32,	`longblob`	Size of each block
`qStarts`	0,	`longblob`	Start of each block in query.
`tStarts`	228256169,	`longblob`	Start of each block in target.

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via xenoMrna.qName) hgFixed.gbMiscDiff.acc (via xenoMrna.qName) hgFixed.gbSeq.acc (via xenoMrna.qName) hgFixed.gbWarn.acc (via xenoMrna.qName) hgFixed.imageClone.acc (via xenoMrna.qName) panTro3.all_est.qName (via xenoMrna.qName) panTro3.all_mrna.qName (via xenoMrna.qName) panTro3.refGene.name (via xenoMrna.qName) panTro3.refSeqAli.qName (via xenoMrna.qName) panTro3.xenoRefFlat.name (via xenoMrna.qName) panTro3.xenoRefGene.name (via xenoMrna.qName) panTro3.xenoRefSeqAli.qName (via xenoMrna.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	31	1	0	0	0	0	+-	JD469940	32	0	32	chr1	228333871	77670	77702	1	32,	0,	228256169,
585	32	0	0	0	0	0	+-	JD483070	32	0	32	chr1	228333871	77670	77702	1	32,	0,	228256169,
585	32	0	0	0	0	0	+-	JD454660	32	0	32	chr1	228333871	77695	77727	1	32,	0,	228256144,
585	32	0	0	0	0	0	+-	JD496763	32	0	32	chr1	228333871	77772	77804	1	32,	0,	228256067,
585	140	3	0	0	0	0	++	LE331996	619	167	310	chr1	228333871	77862	78005	1	143,	167,	77862,
585	31	1	0	0	0	0	+-	JD200225	32	0	32	chr1	228333871	77929	77961	1	32,	0,	228255910,
585	32	0	0	0	0	0	+-	JD492450	32	0	32	chr1	228333871	77960	77992	1	32,	0,	228255879,
585	31	1	0	0	0	0	+-	JD485719	32	0	32	chr1	228333871	78636	78668	1	32,	0,	228255203,
73	958	35	6	1105	6	24399	+-	AL137655	3617	709	2807	chr1	228333871	130136	155528	7	103,96,180,68,36,266,244,	709,1149,1555,1753,2087,2187,2563,	228178343,228178754,228192988,228194027,228196926,228202795,228203491,
585	32	0	0	0	0	0	+-	JD262631	32	0	32	chr1	228333871	130169	130201	1	32,	0,	228203670,

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