Schema for all

Schema for all_est

Database: panTro1 Primary Table: all_est Row Count: 19,062 Data last updated: 2016-04-16
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	631	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	664	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	1	`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`	1	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	1	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	5	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	12512	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AU298520	`varchar(255)`	values	Query sequence name
`qSize`	666	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	666	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	229575298	`int(10) unsigned`	range	Target sequence size
`tStart`	6110978	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	6124155	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	7	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	93,289,19,125,81,24,34,	`longblob`		Size of each block
`qStarts`	0,93,382,401,526,608,632,	`longblob`		Start of each block in query.
`tStarts`	6110978,6111072,6111362,611...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	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) panTro1.all_mrna.qName (via all_est.qName) panTro1.est.qName (via all_est.qName) panTro1.estOrientInfo.name (via all_est.qName) panTro1.intronEst.qName (via all_est.qName) panTro1.refGene.name (via all_est.qName) panTro1.refSeqAli.qName (via all_est.qName) panTro1.xenoMrna.qName (via all_est.qName) panTro1.xenoRefGene.name (via all_est.qName) panTro1.xenoRefSeqAli.qName (via all_est.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
631	664	1	0	1	1	5	12512	-	AU298520	666	0	666	chr1	229575298	6110978	6124155	7	93,289,19,125,81,24,34,	0,93,382,401,526,608,632,	6110978,6111072,6111362,6117473,6122211,6122292,6124121,
631	570	0	0	2	2	2	10705	-	AU297734	606	34	606	chr1	229575298	6111040	6122315	5	16,325,125,81,23,	0,17,342,467,549,	6111040,6111056,6117473,6122211,6122292,
631	524	0	1	0	0	2	10705	-	AU298400	553	28	553	chr1	229575298	6111087	6122317	3	294,125,106,	0,294,419,	6111087,6117473,6122211,
631	442	3	3	2	2	4	12511	-	AU296854	450	0	450	chr1	229575298	6111195	6124154	7	53,133,125,80,21,3,33,	0,54,187,312,392,414,417,	6111195,6111248,6117473,6122211,6122292,6122313,6124121,
652	607	0	0	0	0	5	7948	-	AU298587	716	106	713	chr1	229575298	8867788	8876343	6	152,134,70,59,96,96,	3,155,289,359,418,514,	8867788,8868555,8869410,8871887,8873329,8876247,
652	508	0	0	0	0	5	7948	-	AU297919	617	109	617	chr1	229575298	8867887	8876343	6	53,134,70,59,96,96,	0,53,187,257,316,412,	8867887,8868555,8869410,8871887,8873329,8876247,
652	456	0	0	0	0	4	7333	-	AU297857	583	105	561	chr1	229575298	8868554	8876343	5	135,70,59,96,96,	22,157,227,286,382,	8868554,8869410,8871887,8873329,8876247,
652	350	0	0	1	10	4	7343	-	AU297593	470	110	470	chr1	229575298	8868650	8876343	5	39,70,59,98,84,	0,39,109,168,276,	8868650,8869410,8871887,8873329,8876259,
652	284	1	0	1	1	3	6648	-	AU297247	403	107	393	chr1	229575298	8869410	8876343	4	71,22,96,96,	10,82,104,200,	8869410,8871924,8873329,8876247,
652	228	0	12	2	13	2	4216	-	AU297542	400	111	364	chr1	229575298	8871887	8876343	4	47,81,16,96,	36,95,177,193,	8871887,8873328,8873409,8876247,

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