Schema for all

Schema for all_est

Database: macEug2 Primary Table: all_est Row Count: 417,423 Data last updated: 2017-05-08
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	126	`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`	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`	EX200705	`varchar(255)`	values	Query sequence name
`qSize`	754	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	126	`int(10) unsigned`	range	Alignment end position in query
`tName`	ABQO010000537	`varchar(255)`	values	Target sequence name
`tSize`	252	`int(10) unsigned`	range	Target sequence size
`tStart`	93	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	220	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	8,118,	`longblob`		Size of each block
`qStarts`	0,8,	`longblob`		Start of each block in query.
`tStarts`	93,102,	`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) macEug2.all_mrna.qName (via all_est.qName) macEug2.estOrientInfo.name (via all_est.qName) macEug2.intronEst.qName (via all_est.qName) macEug2.xenoMrna.qName (via all_est.qName) macEug2.xenoRefGene.name (via all_est.qName) macEug2.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
585	126	0	0	0	0	1	1	+	EX200705	754	0	126	ABQO010000537	252	93	220	2	8,118,	0,8,	93,102,
585	404	0	0	0	0	1	172	-	EX207226	757	353	757	ABQO010000622	3834	3197	3773	2	356,48,	0,356,	3197,3725,
585	161	0	0	0	0	1	1	+	EX209958	183	2	163	ABQO010001424	1534	1033	1195	2	28,133,	2,30,	1033,1062,
585	649	2	0	0	0	0	0	+	EX199657	734	0	651	ABQO010002873	807	156	807	1	651,	0,	156,
585	311	2	0	0	0	0	0	+	EX202057	756	0	313	ABQO010002873	807	494	807	1	313,	0,	494,
585	505	2	1	2	2	1	1	+	EX203258	523	0	510	ABQO010005220	1289	245	754	4	403,29,72,4,	0,403,433,506,	245,649,678,750,
585	70	4	0	1	5	4	28	-	EX206828	545	303	382	ABQO010008008	5691	2234	2336	5	17,16,8,10,23,	163,180,201,209,219,	2234,2252,2275,2289,2313,
585	161	0	0	0	0	1	1	+	EX209958	183	2	163	ABQO010009479	930	132	294	2	28,133,	2,30,	132,161,
585	90	0	0	0	0	0	0	-	EX198747	720	74	164	ABQO010009622	2521	1923	2013	1	90,	556,	1923,
585	90	0	0	0	0	0	0	-	EX198844	711	38	128	ABQO010009622	2521	1923	2013	1	90,	583,	1923,

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