Schema for xenoMrna

Database: gasAcu1 Primary Table: xenoMrna Row Count: 5,930,818 Data last updated: 2020-08-19
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`	62	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	19	`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`	2	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	25007	`int(10) unsigned`	Number of bases inserted in target
`strand`	+-	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	JT287781	`varchar(255)`	Query sequence name
`qSize`	305	`int(10) unsigned`	Query sequence size
`qStart`	151	`int(10) unsigned`	Alignment start position in query
`qEnd`	232	`int(10) unsigned`	Alignment end position in query
`tName`	chrI	`varchar(255)`	Target sequence name
`tSize`	28185914	`int(10) unsigned`	Target sequence size
`tStart`	79	`int(10) unsigned`	Alignment start position in target
`tEnd`	25167	`int(10) unsigned`	Alignment end position in target
`blockCount`	3	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	36,2,43,	`longblob`	Size of each block
`qStarts`	151,187,189,	`longblob`	Start of each block in query.
`tStarts`	28160747,28160912,28185792,	`longblob`	Start of each block in target.

Connected Tables and Joining Fields


	gasAcu1.all_est.qName (via xenoMrna.qName) gasAcu1.all_mrna.qName (via xenoMrna.qName) gasAcu1.refGene.name (via xenoMrna.qName) gasAcu1.refSeqAli.qName (via xenoMrna.qName) gasAcu1.xenoRefGene.name (via xenoMrna.qName) gasAcu1.xenoRefSeqAli.qName (via xenoMrna.qName) 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)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	62	19	0	0	2	25007	+-	JT287781	305	151	232	chrI	28185914	79	25167	3	36,2,43,	151,187,189,	28160747,28160912,28185792,
73	97	26	2	314	2	173621	+-	JI298104	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	97	26	2	314	2	173621	+-	JI298105	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	97	26	2	314	2	173621	+-	JI298107	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	97	26	2	314	2	173621	+-	JI298109	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	97	26	2	314	2	173621	+-	JI298111	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	97	26	2	314	2	173621	+-	JI298118	575	119	556	chrI	28185914	79	173823	3	57,24,42,	119,258,514,	28012091,28160467,28185793,
73	129	42	3	39	4	430711	+-	JT216602	720	441	651	chrI	28185914	79	430961	6	27,36,33,12,21,42,	441,468,504,546,576,609,	27754953,27755295,27755643,27755988,27756000,28185793,
73	129	42	3	39	4	430711	+-	JT326139	1010	767	977	chrI	28185914	79	430961	6	27,36,33,12,21,42,	767,794,830,872,902,935,	27754953,27755295,27755643,27755988,27756000,28185793,
73	129	42	3	39	4	430711	+-	JT466407	861	14	224	chrI	28185914	79	430961	6	27,36,33,12,21,42,	14,41,77,119,149,182,	27754953,27755295,27755643,27755988,27756000,28185793,

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