Schema for intronEst

Database: canFam4 Primary Table: intronEst Row Count: 196,179 Data last updated: 2020-05-06
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	1450	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	390	`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`	2	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	3	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	5	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	7642	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB042265	`varchar(255)`	values	Query sequence name
`qSize`	393	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	393	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	123556469	`int(10) unsigned`	range	Target sequence size
`tStart`	113419652	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	113427684	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	7	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	14,29,54,78,148,52,15,	`longblob`		Size of each block
`qStarts`	0,16,46,100,178,326,378,	`longblob`		Start of each block in query.
`tStarts`	113419652,113419667,1134196...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	canFam4.all_est.qName (via intronEst.qName) canFam4.estOrientInfo.name (via intronEst.qName) hgFixed.gbCdnaInfo.acc (via intronEst.qName) hgFixed.gbSeq.acc (via intronEst.qName) hgFixed.imageClone.acc (via intronEst.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1450	390	0	0	2	3	5	7642	+	AB042265	393	0	393	chr1	123556469	113419652	113427684	7	14,29,54,78,148,52,15,	0,16,46,100,178,326,378,	113419652,113419667,113419696,113421406,113421669,113427616,113427669,
724	249	1	0	0	0	1	8043	-	AB042264	250	0	250	chr19	55516201	18222825	18231118	2	179,71,	0,179,	18222825,18231047,
820	326	1	1	7	8	7	2004	+	AB042266	408	7	343	chr36	31223415	30901648	30903980	14	36,18,45,54,45,46,7,20,7,11,5,18,9,7,	7,44,62,107,161,206,254,261,282,290,301,307,326,336,	30901648,30901684,30902129,30902295,30902804,30903449,30903496,30903902,30903922,30903929,30903941,30903946,30903964,30903973,
856	704	3	0	0	0	3	575	-	AJ536902	729	20	727	chr1	123556469	35609589	35610871	4	71,53,201,382,	2,73,126,327,	35609589,35609938,35610159,35610489,
1053	478	2	0	0	0	1	10080	-	AJ536897	483	0	480	chr1	123556469	61426814	61437374	2	110,370,	3,113,	61426814,61437004,
1225	725	8	0	0	0	5	12315	-	AJ536894	744	11	744	chr1	123556469	83895076	83908124	6	132,109,69,114,104,205,	0,132,241,310,424,528,	83895076,83896133,83896243,83899114,83907130,83907919,
1236	518	1	0	0	0	2	2318	-	AJ536898	528	0	519	chr1	123556469	85425387	85428224	3	339,123,57,	9,348,471,	85425387,85426622,85428167,
1287	379	2	0	0	0	1	3933	-	AJ536895	408	13	394	chr1	123556469	92070321	92074635	2	288,93,	14,302,	92070321,92074542,
589	528	5	0	0	0	6	8846	+	AJ537082	533	0	533	chr10	70643054	633290	642669	7	16,86,90,161,65,91,24,	0,16,102,192,353,418,509,	633290,633713,633890,641562,641968,642273,642645,
601	370	1	2	1	1	2	750	+	AJ537075	432	48	422	chr10	70643054	2164012	2165135	4	6,182,168,17,	48,55,237,405,	2164012,2164018,2164682,2165118,

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