Schema for all

Schema for all_est

Database: monDom4 Primary Table: all_est Row Count: 449 Data last updated: 2016-04-13
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	744	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	623	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	6	`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`	2	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	1674	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	DR038220	`varchar(255)`	values	Query sequence name
`qSize`	630	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	630	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	748055161	`int(10) unsigned`	range	Target sequence size
`tStart`	20864151	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	20866454	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	3	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	343,140,146,	`longblob`		Size of each block
`qStarts`	0,344,484,	`longblob`		Start of each block in query.
`tStarts`	20864151,20864924,20866308,	`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) monDom4.all_mrna.qName (via all_est.qName) monDom4.est.qName (via all_est.qName) monDom4.estOrientInfo.name (via all_est.qName) monDom4.intronEst.qName (via all_est.qName) monDom4.refGene.name (via all_est.qName) monDom4.refSeqAli.qName (via all_est.qName) monDom4.xenoMrna.qName (via all_est.qName) monDom4.xenoRefGene.name (via all_est.qName) monDom4.xenoRefSeqAli.qName (via all_est.qName)

Sample Rows

bin	matches	misMatches	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
744	623	6	0	1	1	2	1674	+	DR038220	630	0	630	chr1	748055161	20864151	20866454	3	343,140,146,	0,344,484,	20864151,20864924,20866308,
744	423	4	0	0	0	3	10822	-	DR038222	446	19	446	chr1	748055161	20867995	20879244	4	47,177,162,41,	0,47,224,386,	20867995,20873907,20878372,20879203,
744	422	5	0	0	0	3	66745	-	DR038222	446	19	446	chr1	748055161	20900165	20967337	4	47,177,162,41,	0,47,224,386,	20900165,20906056,20966466,20967296,
744	625	4	0	1	1	2	1653	+	DR038220	630	0	630	chr1	748055161	20907517	20909799	3	343,140,146,	0,344,484,	20907517,20908290,20909653,
744	508	5	0	0	0	4	5232	-	DR038229	539	26	539	chr1	748055161	20926034	20931779	5	133,35,161,150,34,	0,133,168,329,479,	20926034,20926168,20930491,20931319,20931745,
744	623	6	0	1	1	2	1673	+	DR038220	630	0	630	chr1	748055161	20948444	20950746	3	343,140,146,	0,344,484,	20948444,20949217,20950600,
1441	223	1	0	0	0	0	0	+	DR041732	252	28	252	chr1	748055161	112235056	112235280	1	224,	28,	112235056,
1575	120	0	77	0	0	0	0	-	DR038233	607	0	197	chr1	748055161	129822008	129822205	1	197,	410,	129822008,
2279	211	0	394	0	0	0	0	+	DR038230	631	23	628	chr1	748055161	222105232	222105837	1	605,	23,	222105232,
3092	346	6	0	0	0	1	1381	+	DR038237	364	0	352	chr1	748055161	328636476	328638209	2	88,264,	0,88,	328636476,328637945,

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