Schema for refSeqAli

Database: sarHar1 Primary Table: refSeqAli Row Count: 72 Data last updated: 2016-04-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	601	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	150	`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_105676	`varchar(255)`	values	Query sequence name
`qSize`	150	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	150	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1_GL834484_random	`varchar(255)`	values	Target sequence name
`tSize`	3839433	`int(10) unsigned`	range	Target sequence size
`tStart`	2121689	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	2121839	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	150,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	2121689,	`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) sarHar1.all_mrna.qName (via refSeqAli.qName) sarHar1.mrnaOrientInfo.name (via refSeqAli.qName) sarHar1.refFlat.name (via refSeqAli.qName) sarHar1.refGene.name (via refSeqAli.qName) sarHar1.xenoMrna.qName (via refSeqAli.qName) sarHar1.xenoRefGene.name (via refSeqAli.qName) sarHar1.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows

bin	matches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
601	150	+	NR_105676	150	150	chr1_GL834484_random	3839433	2121689	2121839	1	150,	0,	2121689,
603	110	+	NR_105677	110	110	chr1_GL834637_random	2638213	2485834	2485944	1	110,	0,	2485834,
592	150	+	NR_105678	150	150	chr1_GL834650_random	2003497	1024446	1024596	1	150,	0,	1024446,
604	150	+	NR_105679	150	150	chr1_GL834659_random	3630962	2574239	2574389	1	150,	0,	2574239,
589	150	-	NR_105680	150	150	chr1_GL834685_random	658685	638210	638360	1	150,	0,	638210,
590	150	+	NR_105682	150	150	chr1_GL834730_random	1323300	741011	741161	1	150,	0,	741011,
592	150	+	NR_105683	150	150	chr1_GL834734_random	1590404	1003763	1003913	1	150,	0,	1003763,
592	150	+	NR_105684	150	150	chr1_GL834734_random	1590404	1019941	1020091	1	150,	0,	1019941,
599	150	+	NR_105685	150	150	chr1_GL834769_random	1938635	1909499	1909649	1	150,	0,	1909499,
585	150	+	NR_105686	150	150	chr1_GL834949_random	145045	4221	4371	1	150,	0,	4221,

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