Schema for intronEst

Database: canFam3 Primary Table: intronEst Row Count: 201,670 Data last updated: 2016-06-11
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	1444	`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`	7617	`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`	122678785	`int(10) unsigned`	range	Target sequence size
`tStart`	112634879	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	112642886	`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`	112634879,112634894,1126349...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	canFam3.all_est.qName (via intronEst.qName) canFam3.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
1444	390	0	0	2	3	5	7617	+	AB042265	393	0	393	chr1	122678785	112634879	112642886	7	14,29,54,78,148,52,15,	0,16,46,100,178,326,378,	112634879,112634894,112634923,112636633,112636892,112642818,112642871,
717	249	1	0	0	0	1	8063	-	AB042264	250	0	250	chr19	53741614	17403385	17411698	2	179,71,	0,179,	17403385,17411627,
817	326	1	1	7	8	7	2004	+	AB042266	408	7	343	chr36	30810995	30505606	30507938	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,	30505606,30505642,30506087,30506253,30506762,30507407,30507454,30507860,30507880,30507887,30507899,30507904,30507922,30507931,
854	704	3	0	0	0	3	575	-	AJ536902	729	20	727	chr1	122678785	35372590	35373872	4	71,53,201,382,	2,73,126,327,	35372590,35372939,35373160,35373490,
1049	478	2	0	0	0	1	10079	-	AJ536897	483	0	480	chr1	122678785	60853741	60864300	2	110,370,	3,113,	60853741,60863930,
1219	725	8	0	0	0	5	12332	-	AJ536894	744	11	744	chr1	122678785	83214426	83227491	6	132,109,69,114,104,205,	0,132,241,310,424,528,	83214426,83215483,83215593,83218456,83226497,83227286,
1231	518	1	0	0	0	2	2318	-	AJ536898	528	0	519	chr1	122678785	84744158	84746995	3	339,123,57,	9,348,471,	84744158,84745393,84746938,
1282	379	2	0	0	0	1	3933	-	AJ536895	408	13	394	chr1	122678785	91391619	91395933	2	288,93,	14,302,	91391619,91395840,
587	528	5	0	0	0	6	8847	+	AJ537082	533	0	533	chr10	69331447	281627	291007	7	16,86,90,161,65,91,24,	0,16,102,192,353,418,509,	281627,282050,282227,289900,290306,290611,290983,
598	370	1	2	1	1	2	750	+	AJ537075	432	48	422	chr10	69331447	1810070	1811193	4	6,182,168,17,	48,55,237,405,	1810070,1810076,1810740,1811176,

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