Schema for all

Schema for all_est

Database: gadMor1 Primary Table: all_est Row Count: 340,247 Data last updated: 2016-03-30
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`	141	`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`	0	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	CO541865	`varchar(255)`	values	Query sequence name
`qSize`	767	`int(10) unsigned`	range	Query sequence size
`qStart`	61	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	202	`int(10) unsigned`	range	Alignment end position in query
`tName`	CAEA01000621	`varchar(255)`	values	Target sequence name
`tSize`	2107	`int(10) unsigned`	range	Target sequence size
`tStart`	1287	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	1428	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	141,	`longblob`		Size of each block
`qStarts`	565,	`longblob`		Start of each block in query.
`tStarts`	1287,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	gadMor1.all_mrna.qName (via all_est.qName) gadMor1.estOrientInfo.name (via all_est.qName) gadMor1.intronEst.qName (via all_est.qName) gadMor1.xenoRefGene.name (via all_est.qName) gadMor1.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	repMatches	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	141	0	0	0	0	-	CO541865	767	61	202	CAEA01000621	2107	1287	1428	1	141,	565,	1287,
585	80	0	0	0	0	-	CO542793	771	281	361	CAEA01003413	951	857	937	1	80,	410,	857,
585	208	0	0	1	487	-	CO541553	713	1	209	CAEA01005662	2384	158	853	2	164,44,	504,668,	158,809,
585	190	6	42	1	831	+	CO541767	841	0	238	CAEA01007478	1308	159	1228	2	48,190,	0,48,	159,1038,
585	339	0	27	3	580	-	CO542061	841	1	367	CAEA01008787	1401	91	1037	4	68,94,76,128,	474,542,636,712,	91,531,741,909,
585	416	6	283	0	0	-	CO541706	716	1	706	CAEA01013997	1690	713	1418	1	705,	10,	713,
585	115	0	0	0	0	+	CO542206	762	433	548	CAEA01014596	1327	1212	1327	1	115,	433,	1212,
585	114	2	0	2	239	+	CO541629	728	499	615	CAEA01014821	639	194	549	3	40,41,35,	499,539,580,	194,335,514,
585	187	0	0	1	490	-	CO541569	612	1	188	CAEA01015974	1052	215	892	2	134,53,	424,558,	215,839,
585	104	0	11	0	0	-	CO541673	763	638	753	CAEA01015974	1052	838	953	1	115,	10,	838,

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