Schema for intronEst

Database: monDom5 Primary Table: intronEst Row Count: 164 Data last updated: 2011-03-30
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	661	`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`	10062383	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	10064686	`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`	10062383,10063156,10064540,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via intronEst.qName) hgFixed.gbSeq.acc (via intronEst.qName) hgFixed.imageClone.acc (via intronEst.qName) monDom5.all_est.qName (via intronEst.qName) monDom5.estOrientInfo.name (via intronEst.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
661	623	6	1	1	2	1674	+	DR038220	630	0	630	chr1	748055161	10062383	10064686	3	343,140,146,	0,344,484,	10062383,10063156,10064540,
661	423	4	0	0	3	10822	-	DR038222	446	19	446	chr1	748055161	10066227	10077476	4	47,177,162,41,	0,47,224,386,	10066227,10072139,10076604,10077435,
662	422	5	0	0	3	66745	-	DR038222	446	19	446	chr1	748055161	10098397	10165569	4	47,177,162,41,	0,47,224,386,	10098397,10104288,10164698,10165528,
662	625	4	1	1	2	1653	+	DR038220	630	0	630	chr1	748055161	10105749	10108031	3	343,140,146,	0,344,484,	10105749,10106522,10107885,
662	508	5	0	0	4	5232	-	DR038229	539	26	539	chr1	748055161	10124266	10130011	5	133,35,161,150,34,	0,133,168,329,479,	10124266,10124400,10128723,10129551,10129977,
662	623	6	1	1	2	1673	+	DR038220	630	0	630	chr1	748055161	10146676	10148978	3	343,140,146,	0,344,484,	10146676,10147449,10148832,
3092	346	6	0	0	1	1381	+	DR038237	364	0	352	chr1	748055161	328636476	328638209	2	88,264,	0,88,	328636476,328637945,
3208	734	1	0	0	6	2128	-	DR038231	735	0	735	chr1	748055161	343911809	343914672	7	69,60,90,93,50,154,219,	0,69,129,219,312,362,516,	343911809,343912148,343912300,343913065,343913657,343914298,343914453,
3999	149	0	0	0	1	240	+	DR041725	338	189	338	chr1	748055161	447510898	447511287	2	18,131,	189,207,	447510898,447511156,
3999	234	0	0	0	1	427	-	DR041726	259	25	259	chr1	748055161	447543767	447544428	2	16,218,	0,16,	447543767,447544210,

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