Schema for all

Schema for all_est

Database: mm39 Primary Table: all_est Row Count: 5,269,821 Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	609	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`matches`	118	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	0	`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`	0	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	0	`int(10) unsigned`	Number of bases inserted in target
`strand`	-	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	AA549021	`varchar(255)`	Query sequence name
`qSize`	118	`int(10) unsigned`	Query sequence size
`qStart`	0	`int(10) unsigned`	Alignment start position in query
`qEnd`	118	`int(10) unsigned`	Alignment end position in query
`tName`	chr1	`varchar(255)`	Target sequence name
`tSize`	195154279	`int(10) unsigned`	Target sequence size
`tStart`	3147192	`int(10) unsigned`	Alignment start position in target
`tEnd`	3147310	`int(10) unsigned`	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	118,	`longblob`	Size of each block
`qStarts`	0,	`longblob`	Start of each block in query.
`tStarts`	3147192,	`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) mm39.all_mrna.qName (via all_est.qName) mm39.estOrientInfo.name (via all_est.qName) mm39.refGene.name (via all_est.qName) mm39.refSeqAli.qName (via all_est.qName) mm39.xenoMrna.qName (via all_est.qName) mm39.xenoRefGene.name (via all_est.qName) mm39.xenoRefSeqAli.qName (via all_est.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
609	118	0	0	0	0	0	-	AA549021	118	0	118	chr1	195154279	3147192	3147310	1	118,	0,	3147192,
609	54	0	0	0	0	0	-	AA624004	75	0	54	chr1	195154279	3147247	3147301	1	54,	21,	3147247,
609	45	0	0	0	0	0	-	AA682002	65	20	65	chr1	195154279	3147263	3147308	1	45,	0,	3147263,
609	245	7	2	30	2	42	+	AA517615	500	0	282	chr1	195154279	3224445	3224739	4	20,201,18,13,	0,20,250,269,	3224445,3224484,3224708,3224726,
609	169	4	0	0	1	1	+	AA538072	180	0	173	chr1	195154279	3226103	3226277	2	157,16,	0,157,	3226103,3226261,
609	45	0	0	0	0	0	-	AA682002	65	20	65	chr1	195154279	3245853	3245898	1	45,	0,	3245853,
609	157	2	0	0	0	0	-	AA623689	159	0	159	chr1	195154279	3246054	3246213	1	159,	0,	3246054,
609	161	0	0	0	0	0	-	AA672930	170	9	170	chr1	195154279	3246054	3246215	1	161,	0,	3246054,
611	148	0	0	0	0	0	+	AA174649	154	6	154	chr1	195154279	3417150	3417298	1	148,	6,	3417150,
613	378	1	0	0	0	0	-	AA691122	379	0	379	chr1	195154279	3683127	3683506	1	379,	0,	3683127,

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