Schema for all

Schema for all_est

Database: cb3 Primary Table: all_est Row Count: 2,427 Data last updated: 2016-05-27
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	73	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	203	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	1	`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`	3	`int(10) unsigned`	range	Number of 'N' bases
`qNumInsert`	2	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	2	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	2	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	49	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	R04897	`varchar(255)`	values	Query sequence name
`qSize`	216	`int(10) unsigned`	range	Query sequence size
`qStart`	7	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	216	`int(10) unsigned`	range	Alignment end position in query
`tName`	chrI	`varchar(255)`	values	Target sequence name
`tSize`	11274843	`int(10) unsigned`	range	Target sequence size
`tStart`	393072	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	393328	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	96,30,4,77,	`longblob`		Size of each block
`qStarts`	7,104,134,139,	`longblob`		Start of each block in query.
`tStarts`	393072,393170,393247,393251,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	cb3.all_mrna.qName (via all_est.qName) cb3.est.qName (via all_est.qName) cb3.estOrientInfo.name (via all_est.qName) cb3.intronEst.qName (via all_est.qName) cb3.xenoMrna.qName (via all_est.qName) cb3.xenoRefGene.name (via all_est.qName) cb3.xenoRefSeqAli.qName (via all_est.qName) hgFixed.gbCdnaInfo.acc (via all_est.qName) hgFixed.gbMiscDiff.acc (via all_est.qName) hgFixed.gbSeq.acc (via all_est.qName) hgFixed.gbWarn.acc (via all_est.qName) hgFixed.imageClone.acc (via all_est.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
73	203	1	3	2	2	2	49	+	R04897	216	7	216	chrI	11274843	393072	393328	4	96,30,4,77,	7,104,134,139,	393072,393170,393247,393251,
588	302	3	2	7	8	2	2580	+	R03381	315	0	315	chrI	11274843	487323	490210	10	40,36,141,43,7,12,9,7,8,4,	0,41,77,218,262,271,284,294,302,311,	487323,487363,489648,490120,490163,490170,490182,490191,490198,490206,
588	300	1	3	0	0	2	3	-	R03382	304	0	304	chrI	11274843	493342	493649	3	140,97,67,	0,140,237,	493342,493484,493582,
593	331	1	2	2	2	1	48	+	R05259	336	0	336	chrI	11274843	1089935	1090317	4	228,98,4,4,	0,228,327,332,	1089935,1090211,1090309,1090313,
593	299	0	1	3	4	3	50	+	R03974	304	0	304	chrI	11274843	1089940	1090290	6	5,12,204,45,8,26,	0,5,19,223,269,278,	1089940,1089946,1089959,1090211,1090256,1090264,
593	348	0	0	7	9	4	56	-	R03857	363	3	360	chrI	11274843	1090327	1090731	10	7,6,4,7,4,137,70,53,42,18,	3,13,20,25,33,38,176,246,299,342,	1090327,1090335,1090341,1090345,1090352,1090356,1090495,1090566,1090671,1090713,
593	308	0	1	3	3	3	54	-	R05047	312	0	312	chrI	11274843	1090334	1090697	7	12,5,5,137,71,53,26,	0,13,19,25,162,233,286,	1090334,1090346,1090351,1090356,1090494,1090566,1090671,
593	297	0	2	1	1	1	46	-	R03680	304	4	304	chrI	11274843	1090379	1090724	3	185,61,53,	0,186,247,	1090379,1090564,1090671,
593	264	3	5	0	0	0	0	+	R03322	272	0	272	chrI	11274843	1169970	1170242	1	272,	0,	1169970,
593	264	4	0	0	0	1	895	-	R03323	268	0	268	chrI	11274843	1175433	1176596	2	156,112,	0,156,	1175433,1176484,

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