Schema for intronEst

Database: anoGam3 Primary Table: intronEst Row Count: 71,821 Data last updated: 2018-01-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	664	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	565	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	9	`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`	3	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	11	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	5	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	155	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AA413325	`varchar(255)`	values	Query sequence name
`qSize`	590	`int(10) unsigned`	range	Query sequence size
`qStart`	5	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	590	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr2L	`varchar(255)`	values	Target sequence name
`tSize`	49364325	`int(10) unsigned`	range	Target sequence size
`tStart`	10356718	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	10357447	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	8	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	169,22,53,218,37,37,33,5,	`longblob`		Size of each block
`qStarts`	5,183,205,258,477,514,551,585,	`longblob`		Start of each block in query.
`tStarts`	10356718,10356898,10357061,...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	anoGam3.all_est.qName (via intronEst.qName) anoGam3.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	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
664	565	9	0	3	11	5	155	+	AA413325	590	5	590	chr2L	49364325	10356718	10357447	8	169,22,53,218,37,37,33,5,	5,183,205,258,477,514,551,585,	10356718,10356898,10357061,10357115,10357333,10357371,10357409,10357442,
714	565	12	0	3	18	9	1290	-	AA413348	635	20	615	chr2L	49364325	17002880	17004747	11	5,4,27,14,57,24,9,55,60,262,60,	20,25,29,56,79,136,167,176,233,293,555,	17002880,17002887,17002892,17002920,17002950,17003008,17003044,17003054,17003109,17003170,17004687,
831	593	2	40	1	6	11	2706	+	AA413352	660	19	660	chr2L	49364325	32370994	32374335	12	84,187,64,158,34,34,3,30,13,11,7,10,	19,103,290,354,512,546,580,583,613,626,637,650,	32370994,32371092,32371280,32373272,32374176,32374211,32374246,32374250,32374281,32374295,32374308,32374325,
868	283	0	0	0	0	4	79	+	AA413354	300	17	300	chr2L	49364325	37127399	37127761	5	41,7,195,26,14,	17,58,65,260,286,	37127399,37127516,37127524,37127720,37127747,
938	552	2	0	0	0	8	379	-	AA413355	554	0	554	chr2L	49364325	46316511	46317444	9	5,7,40,284,14,38,8,19,139,	0,5,12,52,336,350,388,396,415,	46316511,46316518,46316526,46316571,46316856,46316872,46316911,46316920,46317305,
590	265	2	0	0	0	4	115	-	AA413315	309	0	267	chr2R	61545105	737046	737428	5	14,14,3,78,158,	42,56,70,73,151,	737046,737061,737076,737080,737270,
666	285	1	0	2	2	5	484	-	AA413317	305	17	305	chr2R	61545105	10622601	10623371	8	9,7,13,9,58,30,131,29,	0,10,17,31,40,98,128,259,	10622601,10622610,10622618,10622631,10622641,10622701,10622732,10623342,
90	457	2	19	4	14	10	9589	-	AA413320	541	19	511	chr2R	61545105	18211113	18221180	12	8,18,10,15,15,4,41,22,61,7,64,213,	30,45,64,74,89,104,109,155,177,238,245,309,	18211113,18211129,18211150,18211162,18211178,18211194,18211198,18211245,18220823,18220885,18220902,18220967,
823	257	2	0	1	2	7	85	-	AA413323	277	16	277	chr2R	61545105	31233914	31234258	8	7,7,5,12,15,94,56,63,	0,7,16,21,33,48,142,198,	31233914,31233922,31233933,31233940,31233953,31233969,31234064,31234195,
653	287	1	0	1	5	4	72	+	AA413338	310	17	310	chr3L	41963435	8990315	8990675	5	137,48,80,13,10,	17,154,202,282,300,	8990315,8990512,8990561,8990643,8990665,

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