Schema for all

Schema for all_est

Database: calJac3 Primary Table: all_est Row Count: 370,563 Data last updated: 2016-06-11
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	606	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	640	`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`	40	`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`	1	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	1	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	EH381499	`varchar(255)`	values	Query sequence name
`qSize`	680	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	680	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	210400635	`int(10) unsigned`	range	Target sequence size
`tStart`	2867115	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	2867796	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	666,14,	`longblob`		Size of each block
`qStarts`	0,666,	`longblob`		Start of each block in query.
`tStarts`	2867115,2867782,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	calJac3.all_mrna.qName (via all_est.qName) calJac3.estOrientInfo.name (via all_est.qName) calJac3.intronEst.qName (via all_est.qName) calJac3.refGene.name (via all_est.qName) calJac3.refSeqAli.qName (via all_est.qName) calJac3.xenoMrna.qName (via all_est.qName) calJac3.xenoRefGene.name (via all_est.qName) calJac3.xenoRefSeqAli.qName (via all_est.qName) hgFixed.gbCdnaInfo.acc (via all_est.qName) hgFixed.gbMiscDiff.acc (via all_est.qName) hgFixed.gbSeq.acc (via all_est.qName) hgFixed.gbWarn.acc (via all_est.qName) hgFixed.imageClone.acc (via all_est.qName)

Sample Rows

bin	matches	misMatches	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
606	640	0	40	0	0	1	1	+	EH381499	680	0	680	chr1	210400635	2867115	2867796	2	666,14,	0,666,	2867115,2867782,
662	675	1	0	1	1	0	0	-	EH381284	680	0	677	chr1	210400635	10139230	10139906	2	150,526,	3,154,	10139230,10139380,
680	661	8	0	2	11	2	9	+	EH382042	680	0	680	chr1	210400635	12579399	12580077	3	21,608,40,	0,23,640,	12579399,12579421,12580037,
685	679	1	0	0	0	0	0	+	EH381231	680	0	680	chr1	210400635	13146878	13147558	1	680,	0,	13146878,
695	679	1	0	0	0	0	0	+	EH381306	680	0	680	chr1	210400635	14539647	14540327	1	680,	0,	14539647,
695	670	10	0	0	0	0	0	+	EH382325	680	0	680	chr1	210400635	14539657	14540337	1	680,	0,	14539657,
696	154	0	523	2	2	2	2	-	EH380505	680	1	680	chr1	210400635	14648290	14648969	5	637,4,23,5,8,	0,638,642,666,671,	14648290,14648927,14648932,14648955,14648961,
714	679	0	0	0	0	0	0	-	EH380422	680	0	679	chr1	210400635	16929035	16929714	1	679,	1,	16929035,
723	643	2	31	0	0	1	1	+	EH381948	680	4	680	chr1	210400635	18192587	18193264	2	663,13,	4,667,	18192587,18193251,
751	634	8	38	0	0	1	1	-	EH381018	680	0	680	chr1	210400635	21805995	21806676	2	9,671,	0,9,	21805995,21806005,

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