Schema for intronEst

Database: susScr3 Primary Table: intronEst Row Count: 804,783 Data last updated: 2015-04-04
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	178	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`matches`	363	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	1	`int(10) unsigned`	Number of bases that don't match
`repMatches`	0	`int(10) unsigned`	Number of bases that match but are part of repeats
`nCount`	0	`int(10) unsigned`	Number of 'N' bases
`qNumInsert`	0	`int(10) unsigned`	Number of inserts in query
`qBaseInsert`	0	`int(10) unsigned`	Number of bases inserted in query
`tNumInsert`	4	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	3761	`int(10) unsigned`	Number of bases inserted in target
`strand`	+	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	AA056913	`varchar(255)`	Query sequence name
`qSize`	364	`int(10) unsigned`	Query sequence size
`qStart`	0	`int(10) unsigned`	Alignment start position in query
`qEnd`	364	`int(10) unsigned`	Alignment end position in query
`tName`	chr1	`varchar(255)`	Target sequence name
`tSize`	315321322	`int(10) unsigned`	Target sequence size
`tStart`	110359280	`int(10) unsigned`	Alignment start position in target
`tEnd`	110363405	`int(10) unsigned`	Alignment end position in target
`blockCount`	5	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	62,104,110,44,44,	`longblob`	Size of each block
`qStarts`	0,62,166,276,320,	`longblob`	Start of each block in query.
`tStarts`	110359280,110359907,1103631...	`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) susScr3.all_est.qName (via intronEst.qName) susScr3.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
178	363	1	0	0	0	0	4	3761	+	AA056913	364	0	364	chr1	315321322	110359280	110363405	5	62,104,110,44,44,	0,62,166,276,320,	110359280,110359907,110363115,110363316,110363361,
922	299	1	15	7	0	0	1	118	+	AA063653	328	6	328	chr12	63588571	44259371	44259811	2	225,97,	6,231,	44259371,44259714,
1377	401	0	0	6	0	0	2	2545	+	AA056907	413	0	407	chr13	218635234	103869575	103872527	3	100,173,134,	0,100,273,	103869575,103870720,103872393,
1552	311	3	0	10	2	2	1	25908	-	AA063657	394	68	394	chr13	218635234	126825924	126852156	4	48,31,37,208,	0,49,81,118,	126825924,126825972,126826003,126851948,
1714	506	1	0	3	1	1	4	18992	+	AA056905	512	1	512	chr13	218635234	148057924	148077426	5	93,46,153,120,98,	1,94,140,293,414,	148057924,148060953,148074331,148077206,148077328,
1714	447	0	0	0	1	1	2	13290	-	AA056906	448	0	448	chr13	218635234	148077429	148091166	4	83,322,14,28,	0,83,406,420,	148077429,148079064,148079386,148091138,
2057	314	1	0	2	0	0	1	147	+	AA063669	352	15	332	chr13	218635234	192982328	192982792	2	159,158,	15,174,	192982328,192982634,
1032	282	1	0	3	0	0	2	3709	-	AA063656	321	7	293	chr14	153851969	58649975	58653970	3	67,147,72,	28,95,242,	58649975,58653122,58653898,
187	415	8	0	2	4	6	5	2509	-	AA063658	443	7	438	chr14	153851969	120060050	120062984	8	10,8,37,91,105,43,70,61,	5,17,26,65,156,261,305,375,	120060050,120060061,120060069,120060107,120062033,120062357,120062400,120062923,
1026	405	2	0	5	4	6	3	9377	+	AA056887	440	22	440	chr17	69701581	57883119	57892908	7	129,12,126,83,21,29,12,	22,154,166,292,376,398,428,	57883119,57883250,57891338,57892763,57892846,57892867,57892896,

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