Schema for all

Schema for all_est

Database: oreNil2 Primary Table: all_est Row Count: 129,732 Data last updated: 2016-05-25
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`	149	`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`	16	`int(10) unsigned`	range	Number of bases that match but are part of repeats
`nCount`	1	`int(10) unsigned`	range	Number of 'N' bases
`qNumInsert`	3	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	4	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	2	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	6	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AI001486	`varchar(255)`	values	Query sequence name
`qSize`	171	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	171	`int(10) unsigned`	range	Alignment end position in query
`tName`	AERX01074241-1	`varchar(255)`	values	Target sequence name
`tSize`	2925	`int(10) unsigned`	range	Target sequence size
`tStart`	2341	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	2514	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	4	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	137,16,8,6,	`longblob`		Size of each block
`qStarts`	0,138,155,165,	`longblob`		Start of each block in query.
`tStarts`	2341,2478,2496,2508,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	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) oreNil2.all_mrna.qName (via all_est.qName) oreNil2.estOrientInfo.name (via all_est.qName) oreNil2.intronEst.qName (via all_est.qName) oreNil2.refGene.name (via all_est.qName) oreNil2.refSeqAli.qName (via all_est.qName) oreNil2.xenoRefGene.name (via all_est.qName) oreNil2.xenoRefSeqAli.qName (via all_est.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
585	149	1	16	1	3	4	2	6	+	AI001486	171	0	171	AERX01074241-1	2925	2341	2514	4	137,16,8,6,	0,138,155,165,	2341,2478,2496,2508,
585	149	1	16	1	3	4	2	6	+	AI001486	171	0	171	AERX01074242-1	2925	2341	2514	4	137,16,8,6,	0,138,155,165,	2341,2478,2496,2508,
594	89	0	19	1	2	3	2	5	-	AI001654	123	0	112	GL831181-1	4215586	1255881	1255995	4	16,57,16,20,	11,29,86,103,	1255881,1255901,1255959,1255975,
591	239	0	66	0	3	4	3	3	+	AI001584	334	10	319	GL831184-1	4048619	831451	831759	7	4,198,26,50,12,4,11,	10,15,213,240,292,304,308,	831451,831455,831654,831680,831730,831743,831748,
591	167	3	19	0	0	0	5	6	-	AI001585	189	0	189	GL831184-1	4048619	832380	832575	6	20,3,18,7,136,5,	0,20,23,41,48,184,	832380,832402,832406,832425,832433,832570,
603	115	4	23	6	0	0	3	3	+	AI001707	188	0	148	GL831184-1	4048619	2475873	2476024	4	9,104,31,4,	0,9,113,144,	2475873,2475883,2475988,2476020,
603	20	1	54	0	1	1	0	0	-	AI001706	147	13	89	GL831184-1	4048619	2476353	2476428	2	53,22,	58,112,	2476353,2476406,
601	62	0	53	0	1	1	2	2	+	AI001709	135	8	124	GL831204-1	3450071	2204346	2204463	4	20,16,60,19,	8,29,45,105,	2204346,2204366,2204383,2204444,
601	91	0	38	0	0	0	1	33	-	AI001708	129	0	129	GL831204-1	3450071	2204874	2205036	2	11,118,	0,11,	2204874,2204918,
605	328	6	30	6	0	0	1	1	+	AI001544	430	10	380	GL831204-1	3450071	2636149	2636520	2	174,196,	10,184,	2636149,2636324,

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