Schema for all

Schema for all_est

Database: ponAbe3 Primary Table: all_est Row Count: 50,531 Data last updated: 2018-03-29
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`	436	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	4	`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`	18	`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`	2	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	13902	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	CR791558	`varchar(255)`	values	Query sequence name
`qSize`	459	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	459	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	227913704	`int(10) unsigned`	range	Target sequence size
`tStart`	3477	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	17837	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	106,224,64,64,	`longblob`		Size of each block
`qStarts`	0,107,331,395,	`longblob`		Start of each block in query.
`tStarts`	3477,3583,7403,17773,	`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) ponAbe3.all_mrna.qName (via all_est.qName) ponAbe3.estOrientInfo.name (via all_est.qName) ponAbe3.intronEst.qName (via all_est.qName) ponAbe3.refGene.name (via all_est.qName) ponAbe3.refSeqAli.qName (via all_est.qName) ponAbe3.xenoRefGene.name (via all_est.qName) ponAbe3.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	436	4	18	1	1	2	13902	-	CR791558	459	0	459	chr1	227913704	3477	17837	4	106,224,64,64,	0,107,331,395,	3477,3583,7403,17773,
585	205	1	0	0	0	0	0	+	CR787192	210	4	210	chr1	227913704	66737	66943	1	206,	4,	66737,
585	750	8	3	1	1	3	1154	+	CR765535	762	0	762	chr1	227913704	67049	68964	5	405,49,90,189,28,	0,405,454,544,734,	67049,68138,68316,68747,68936,
585	621	6	0	1	1	1	343	+	CR539117	629	1	629	chr1	227913704	97657	98627	3	41,558,28,	1,42,601,	97657,98041,98599,
591	630	1	0	0	0	0	0	+	CR542427	644	13	644	chr1	227913704	907281	907912	1	631,	13,	907281,
591	428	1	0	0	0	0	0	+	CR766100	429	0	429	chr1	227913704	907342	907771	1	429,	0,	907342,
592	428	1	0	0	0	0	0	-	CR766100	429	0	429	chr1	227913704	952480	952909	1	429,	0,	952480,
595	663	3	0	2	4	0	0	+	CR543026	670	0	670	chr1	227913704	1342090	1342756	3	212,188,266,	0,213,404,	1342090,1342302,1342490,
596	428	1	0	0	0	0	0	+	CR766100	429	0	429	chr1	227913704	1467079	1467508	1	429,	0,	1467079,
596	508	1	0	0	0	2	2	-	CR540994	509	0	509	chr1	227913704	1467858	1468369	3	127,308,74,	0,127,435,	1467858,1467986,1468295,

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