Schema for refSeqAli

Database: ornAna2 Primary Table: refSeqAli Row Count: 705 Data last updated: 2020-02-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	641	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	87	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	0	`int(10) unsigned`	range	Number of bases that don't match
`repMatches`	0	`int(10) unsigned`	range	Number of bases that match but are part of repeats
`nCount`	0	`int(10) unsigned`	range	Number of 'N' bases
`qNumInsert`	0	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	0	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	NR_034618	`varchar(255)`	values	Query sequence name
`qSize`	87	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	87	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	47594283	`int(10) unsigned`	range	Target sequence size
`tStart`	7455188	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	7455275	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	87,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	7455188,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via refSeqAli.qName) hgFixed.gbMiscDiff.acc (via refSeqAli.qName) hgFixed.gbSeq.acc (via refSeqAli.qName) hgFixed.gbWarn.acc (via refSeqAli.qName) hgFixed.imageClone.acc (via refSeqAli.qName) hgFixed.refLink.mrnaAcc (via refSeqAli.qName) hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName) hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName) knownGeneV39.kgXref.refseq (via refSeqAli.qName) knownGeneV39.knownToRefSeq.value (via refSeqAli.qName) ornAna2.all_est.qName (via refSeqAli.qName) ornAna2.all_mrna.qName (via refSeqAli.qName) ornAna2.mrnaOrientInfo.name (via refSeqAli.qName) ornAna2.refFlat.name (via refSeqAli.qName) ornAna2.refGene.name (via refSeqAli.qName) ornAna2.xenoRefGene.name (via refSeqAli.qName) ornAna2.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows

bin	matches	nCount	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
641	87	0	-	NR_034618	87	87	chr1	47594283	7455188	7455275	1	87,	0,	7455188,
711	120	0	-	NR_034619	120	120	chr1	47594283	16589755	16589875	1	120,	0,	16589755,
713	126	1	-	NR_034620	129	127	chr1	47594283	16822265	16822392	1	127,	2,	16822265,
745	145	0	+	NR_034621	145	145	chr1	47594283	21080347	21080492	1	145,	0,	21080347,
805	126	0	-	NR_034622	126	126	chr1	47594283	28887188	28887314	1	126,	0,	28887188,
808	94	0	+	NR_034623	94	94	chr1	47594283	29293792	29293886	1	94,	0,	29293792,
613	128	0	+	NR_034624	128	128	chr10	11243762	3704099	3704227	1	128,	0,	3704099,
619	100	0	-	NR_034950	100	100	chr10	11243762	4559451	4559551	1	100,	0,	4559451,
619	109	0	-	NR_034625	109	109	chr10	11243762	4568762	4568871	1	109,	0,	4568762,
619	131	0	-	NR_034626	131	131	chr10	11243762	4569066	4569197	1	131,	0,	4569066,

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