Schema for all

Schema for all_est

Database: rheMac10 Primary Table: all_est Row Count: 82,003 Data last updated: 2019-07-03
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	1796	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	301	`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`	3	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	13624	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB471888	`varchar(255)`	values	Query sequence name
`qSize`	301	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	301	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	223616942	`int(10) unsigned`	range	Target sequence size
`tStart`	158799220	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	158813145	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	73,76,106,46,	`longblob`		Size of each block
`qStarts`	0,73,149,255,	`longblob`		Start of each block in query.
`tStarts`	158799220,158810177,1588116...	`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) rheMac10.all_mrna.qName (via all_est.qName) rheMac10.estOrientInfo.name (via all_est.qName) rheMac10.intronEst.qName (via all_est.qName) rheMac10.refGene.name (via all_est.qName) rheMac10.refSeqAli.qName (via all_est.qName) rheMac10.xenoRefGene.name (via all_est.qName) rheMac10.xenoRefSeqAli.qName (via all_est.qName)

Sample Rows

bin	matches	misMatches	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1796	301	0	3	13624	-	AB471888	301	0	301	chr1	223616942	158799220	158813145	4	73,76,106,46,	0,73,149,255,	158799220,158810177,158811666,158813099,
1796	393	1	4	13531	-	AB471889	394	0	394	chr1	223616942	158799220	158813145	5	73,93,76,106,46,	0,73,166,242,348,	158799220,158806294,158810177,158811666,158813099,
1091	98	0	0	0	-	AF089732	98	0	98	chr1	223616942	66445487	66445585	1	98,	0,	66445487,
1328	185	0	0	0	+	AF089889	185	0	185	chr1	223616942	97454639	97454824	1	185,	0,	97454639,
1476	219	3	0	0	+	AF159450	222	0	222	chr1	223616942	116891439	116891661	1	222,	0,	116891439,
691	159	1	0	0	+	AF075126	165	0	160	chr11	133066086	14017966	14018126	1	160,	0,	14017966,
960	278	1	0	0	+	AF139027	279	0	279	chr12	130043856	49255800	49256079	1	279,	0,	49255800,
1091	284	2	0	0	+	AF075122	293	6	292	chr12	130043856	66349756	66350042	1	286,	6,	66349756,
1165	253	0	0	0	+	AF148885	253	0	253	chr12	130043856	76116289	76116542	1	253,	0,	76116289,
1165	380	2	2	179	-	AF140287	382	0	382	chr12	130043856	76149498	76150059	3	262,113,7,	0,262,375,	76149498,76149763,76150052,

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