Schema for all

Schema for all_est

Database: xenTro9 Primary Table: all_est Row Count: 1,277,971 Data last updated: 2017-03-29
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	586	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`matches`	84	`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`	AL775807	`varchar(255)`	Query sequence name
`qSize`	84	`int(10) unsigned`	Query sequence size
`qStart`	0	`int(10) unsigned`	Alignment start position in query
`qEnd`	84	`int(10) unsigned`	Alignment end position in query
`tName`	chr1	`varchar(255)`	Target sequence name
`tSize`	194866763	`int(10) unsigned`	Target sequence size
`tStart`	179519	`int(10) unsigned`	Alignment start position in target
`tEnd`	179603	`int(10) unsigned`	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	84,	`longblob`	Size of each block
`qStarts`	0,	`longblob`	Start of each block in query.
`tStarts`	179519,	`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) xenTro9.all_mrna.qName (via all_est.qName) xenTro9.estOrientInfo.name (via all_est.qName) xenTro9.intronEst.qName (via all_est.qName) xenTro9.refGene.name (via all_est.qName) xenTro9.refSeqAli.qName (via all_est.qName) xenTro9.xenoRefGene.name (via all_est.qName) xenTro9.xenoRefSeqAli.qName (via all_est.qName)

Sample Rows

bin	matches	misMatches	nCount	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
586	84	0	0	0	0	+	AL775807	84	0	84	chr1	194866763	179519	179603	1	84,	0,	179519,
586	547	1	0	0	0	+	AL804149	562	14	562	chr1	194866763	253694	254242	1	548,	14,	253694,
589	394	11	2	0	0	-	AL805176	407	0	407	chr1	194866763	628876	629283	1	407,	0,	628876,
589	633	0	0	2	6	+	AL650304	633	0	633	chr1	194866763	651507	652146	3	250,89,294,	0,250,339,	651507,651760,651852,
589	340	4	0	0	0	-	AL971585	344	0	344	chr1	194866763	654282	654626	1	344,	0,	654282,
590	313	1	0	0	0	-	AL673992	473	159	473	chr1	194866763	655512	655826	1	314,	0,	655512,
590	303	4	0	0	0	-	AL637158	622	315	622	chr1	194866763	655519	655826	1	307,	0,	655519,
594	74	0	0	0	0	+	AL868851	81	7	81	chr1	194866763	1232570	1232644	1	74,	7,	1232570,
594	74	0	0	0	0	-	AL868851	81	7	81	chr1	194866763	1233937	1234011	1	74,	0,	1233937,
597	51	0	1	0	0	+	AL680622	67	14	66	chr1	194866763	1600734	1600786	1	52,	14,	1600734,

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