Schema for intronEst

Database: macFas5 Primary Table: intronEst Row Count: 117,293 Data last updated: 2016-03-31
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	1819	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	301	`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`	0	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	3	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	13640	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB471890	`varchar(255)`	values	Query sequence name
`qSize`	301	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	301	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	227556264	`int(10) unsigned`	range	Target sequence size
`tStart`	161748599	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	161762540	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	73,76,106,46,	`longblob`		Size of each block
`qStarts`	0,73,149,255,	`longblob`		Start of each block in query.
`tStarts`	161748599,161759572,1617610...	`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) macFas5.all_est.qName (via intronEst.qName) macFas5.estOrientInfo.name (via intronEst.qName)

Sample Rows

bin	matches	misMatches	repMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1819	301	0	0	0	0	0	3	13640	-	AB471890	301	0	301	chr1	227556264	161748599	161762540	4	73,76,106,46,	0,73,149,255,	161748599,161759572,161761061,161762494,
1819	301	1	92	0	0	0	4	13547	-	AB471891	394	0	394	chr1	227556264	161748599	161762540	5	73,93,76,106,46,	0,73,166,242,348,	161748599,161755689,161759572,161761061,161762494,
604	651	4	0	1	2	26	3	1034	+	BB875595	682	0	682	chr1	227556264	2533471	2535161	6	30,20,139,406,45,16,	0,30,50,214,620,666,	2533471,2533502,2533523,2533662,2535100,2535145,
606	696	8	0	0	1	4	2	8221	-	BB886550	719	11	719	chr1	227556264	2795284	2804209	4	44,56,417,187,	0,44,100,521,	2795284,2795329,2803605,2804022,
606	680	8	0	2	3	7	3	8222	-	BB877489	734	37	734	chr1	227556264	2795293	2804205	6	8,6,77,417,145,37,	0,8,15,92,513,660,	2795293,2795302,2795308,2803605,2804022,2804168,
645	675	5	0	0	1	3	9	20705	+	BB881382	693	10	693	chr1	227556264	7865507	7886892	10	5,26,49,233,60,102,83,58,51,13,	10,15,41,93,326,386,488,571,629,680,	7865507,7865513,7865540,7865591,7867285,7867435,7869043,7871663,7886827,7886879,
645	751	5	0	2	1	5	9	20710	+	BB881576	780	10	773	chr1	227556264	7865507	7886975	10	7,7,10,10,273,60,102,83,58,148,	10,22,29,39,49,322,382,484,567,625,	7865507,7865521,7865529,7865540,7865551,7867285,7867435,7869043,7871663,7886827,
645	706	2	0	1	1	3	8	20706	+	BB888653	712	0	712	chr1	227556264	7865512	7886927	9	9,10,14,273,60,102,83,58,100,	0,12,22,36,309,369,471,554,612,	7865512,7865525,7865536,7865551,7867285,7867435,7869043,7871663,7886827,
645	706	1	0	1	2	5	8	20707	+	BB889596	713	0	713	chr1	227556264	7865513	7886928	10	7,10,14,38,235,60,102,83,58,101,	0,11,21,35,74,309,369,471,554,612,	7865513,7865525,7865536,7865551,7865589,7867285,7867435,7869043,7871663,7886827,
645	701	3	0	1	0	0	7	20702	+	BB886985	706	1	706	chr1	227556264	7865518	7886925	8	20,11,273,60,102,83,58,98,	1,21,32,305,365,467,550,608,	7865518,7865539,7865551,7867285,7867435,7869043,7871663,7886827,

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