Schema for intronEst

Database: apiMel2 Primary Table: intronEst Row Count: 36,972 Data last updated: 2016-06-08
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	471	`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`	28	`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`	1	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	77	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	DB755625	`varchar(255)`	values	Query sequence name
`qSize`	499	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	499	`int(10) unsigned`	range	Alignment end position in query
`tName`	Group1	`varchar(255)`	values	Target sequence name
`tSize`	25433307	`int(10) unsigned`	range	Target sequence size
`tStart`	589	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	1165	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	155,344,	`longblob`		Size of each block
`qStarts`	0,155,	`longblob`		Start of each block in query.
`tStarts`	589,821,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	apiMel2.all_est.qName (via intronEst.qName) apiMel2.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
585	471	0	28	0	0	1	77	+	DB755625	499	0	499	Group1	25433307	589	1165	2	155,344,	0,155,	589,821,
585	532	1	0	0	0	2	241	-	BI511561	541	8	541	Group1	25433307	2796	3570	3	149,145,239,	0,149,294,	2796,3009,3331,
585	343	1	135	0	0	2	290	+	DB743762	480	1	480	Group1	25433307	4650	5419	3	362,73,44,	1,363,436,	4650,5215,5375,
585	346	0	135	0	0	2	290	+	DB754341	482	1	482	Group1	25433307	4650	5421	3	362,73,46,	1,363,436,	4650,5215,5375,
585	349	1	135	0	0	2	290	+	DB743550	486	1	486	Group1	25433307	4650	5425	3	362,73,50,	1,363,436,	4650,5215,5375,
585	352	4	135	0	0	2	290	+	DB750806	492	1	492	Group1	25433307	4650	5431	3	362,73,56,	1,363,436,	4650,5215,5375,
585	370	14	134	2	3	2	290	+	DB749019	521	0	521	Group1	25433307	4651	5459	5	53,308,73,69,15,	0,54,362,435,506,	4651,4704,5215,5375,5444,
585	385	0	135	0	0	2	290	+	DB744596	520	0	520	Group1	25433307	4651	5461	3	361,73,86,	0,361,434,	4651,5215,5375,
585	393	2	135	0	0	2	290	+	DB749511	538	2	532	Group1	25433307	4659	5479	3	353,73,104,	2,355,428,	4659,5215,5375,
585	491	0	8	0	0	5	544	+	DB780988	499	0	499	Group1	25433307	4984	6027	6	28,73,168,101,81,48,	0,28,101,269,370,451,	4984,5215,5375,5647,5814,5979,

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