Schema for all

Schema for all_est

Database: tupBel1 Primary Table: all_est Row Count: 16,681 Data last updated: 2012-06-12
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	586	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	157	`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`	BI975165	`varchar(255)`	values	Query sequence name
`qSize`	157	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	157	`int(10) unsigned`	range	Alignment end position in query
`tName`	scaffold_115401.1-243207	`varchar(255)`	values	Target sequence name
`tSize`	243207	`int(10) unsigned`	range	Target sequence size
`tStart`	133667	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	133824	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	157,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	133667,	`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) tupBel1.all_mrna.qName (via all_est.qName) tupBel1.estOrientInfo.name (via all_est.qName) tupBel1.intronEst.qName (via all_est.qName) tupBel1.xenoRefGene.name (via all_est.qName) tupBel1.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
586	157	0	0	0	0	0	0	-	BI975165	157	0	157	scaffold_115401.1-243207	243207	133667	133824	1	157,	0,	133667,
585	126	0	0	0	0	0	0	+	BI975165	157	31	157	scaffold_123908.1-121201	121201	72122	72248	1	126,	31,	72122,
585	128	0	0	0	0	1	1	-	BI975165	157	29	157	scaffold_130561.1-52309	52309	48668	48797	2	92,36,	0,92,	48668,48761,
587	128	1	0	0	0	0	0	+	BI975163	129	0	129	scaffold_131641.1-314154	314154	278845	278974	1	129,	0,	278845,
587	179	1	0	2	4	3	4	+	BI975164	184	0	184	scaffold_131641.1-314154	314154	279491	279675	5	30,18,35,62,35,	0,30,49,84,149,	279491,279522,279540,279576,279640,
586	138	0	0	0	0	0	0	-	BI975166	138	0	138	scaffold_137121.1-328252	328252	139170	139308	1	138,	0,	139170,
585	126	0	0	0	0	0	0	+	BI975165	157	31	157	scaffold_143206.1-65253	65253	54316	54442	1	126,	31,	54316,
585	130	0	0	0	0	0	0	-	BI975165	157	27	157	scaffold_1604.1-238595	238595	129896	130026	1	130,	0,	129896,
585	128	0	0	0	0	0	0	+	BI975165	157	29	157	scaffold_16604.1-110902	110902	0	128	1	128,	29,	0,
585	256	2	1	0	0	0	0	+	CF527148	259	0	259	scaffold_100019.1-48780	48780	3834	4093	1	259,	0,	3834,

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