Schema for intronEst

Database: oryCun2 Primary Table: intronEst Row Count: 15,726 Data last updated: 2014-03-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	1243	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	720	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	2	`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`	3	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	14953	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB072617	`varchar(255)`	values	Query sequence name
`qSize`	723	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	723	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr2	`varchar(255)`	values	Target sequence name
`tSize`	174332312	`int(10) unsigned`	range	Target sequence size
`tStart`	86296889	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	86312564	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	5	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	157,219,158,48,140,	`longblob`		Size of each block
`qStarts`	0,158,377,535,583,	`longblob`		Start of each block in query.
`tStarts`	86296889,86297046,86303609,...	`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) oryCun2.all_est.qName (via intronEst.qName) oryCun2.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
1243	720	2	1	1	3	14953	-	AB072617	723	0	723	chr2	174332312	86296889	86312564	5	157,219,158,48,140,	0,158,377,535,583,	86296889,86297046,86303609,86305597,86312424,
972	334	3	0	0	2	1204	+	AF247148	356	0	337	chr17	85008467	50769306	50770847	3	137,134,66,	0,137,271,	50769306,50770176,50770781,
597	324	3	0	0	1	2314	-	AF254947	349	22	349	chrUn0052	1958842	1691373	1694014	2	174,153,	0,174,	1691373,1693861,
834	477	0	0	0	5	7351	-	AF247146	477	0	477	chrX	111700775	32734003	32741831	6	98,64,108,68,82,57,	0,98,162,270,338,420,	32734003,32734296,32740143,32740524,32740770,32741774,
734	154	0	0	0	1	11674	+	AI052991	162	4	158	chr15	109054052	19592767	19604595	2	87,67,	4,91,	19592767,19604528,
700	275	0	0	0	1	2027	+	AI052989	308	3	278	chr2	174332312	15169715	15172017	2	115,160,	3,118,	15169715,15171857,
1623	268	0	0	0	2	7788	+	AI052992	275	2	270	chr7	173684459	136118621	136126677	3	25,189,54,	2,27,216,	136118621,136121493,136126623,
586	227	8	0	0	1	1142	-	BF146289	235	0	235	chrUn0001	14171072	209112	210489	2	120,115,	0,120,	209112,210374,
848	133	1	0	0	1	1150	-	BI389570	134	0	134	chr1	194850757	34528909	34530193	2	36,98,	0,36,	34528909,34530095,
1038	489	7	0	0	4	17396	-	BI993583	514	13	509	chr1	194850757	59434728	59452620	5	103,114,129,62,88,	5,108,222,351,413,	59434728,59437431,59438935,59449151,59452532,

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