Schema for all

Schema for all_est

Database: calJac1 Primary Table: all_est Row Count: 391,331 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`	600	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	675	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	2	`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`	1	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	1	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	EH380431	`varchar(255)`	values	Query sequence name
`qSize`	680	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	677	`int(10) unsigned`	range	Alignment end position in query
`tName`	Contig0	`varchar(255)`	values	Target sequence name
`tSize`	2416186	`int(10) unsigned`	range	Target sequence size
`tStart`	2056416	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	2057094	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	4,673,	`longblob`		Size of each block
`qStarts`	3,7,	`longblob`		Start of each block in query.
`tStarts`	2056416,2056421,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	calJac1.all_mrna.qName (via all_est.qName) calJac1.estOrientInfo.name (via all_est.qName) calJac1.intronEst.qName (via all_est.qName) calJac1.refGene.name (via all_est.qName) calJac1.refSeqAli.qName (via all_est.qName) calJac1.xenoMrna.qName (via all_est.qName) calJac1.xenoRefGene.name (via all_est.qName) calJac1.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	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
600	675	2	0	0	0	1	1	-	EH380431	680	677	Contig0	2416186	2056416	2057094	2	4,673,	3,7,	2056416,2056421,
600	680	0	0	0	0	0	0	-	EH380456	680	680	Contig0	2416186	2056598	2057278	1	680,	0,	2056598,
587	390	0	290	0	0	0	0	+	EH382653	680	680	Contig1	2551648	274032	274712	1	680,	0,	274032,
587	387	3	289	1	1	0	0	+	EH382748	680	680	Contig1	2551648	274035	274714	2	28,651,	0,29,	274035,274063,
590	366	1	313	0	0	2	6683	+	EH380344	680	680	Contig1	2551648	732413	739776	3	357,308,15,	0,357,665,	732413,739452,739761,
590	210	5	465	0	0	1	1	+	EH382784	680	680	Contig1	2551648	739171	739852	2	671,9,	0,671,	739171,739843,
598	440	1	239	0	0	0	0	+	EH380513	680	680	Contig1	2551648	1732698	1733378	1	680,	0,	1732698,
601	654	3	22	0	0	0	0	+	EH382384	680	679	Contig1	2551648	2204672	2205351	1	679,	0,	2204672,
603	670	7	0	3	3	5	398	-	EH382341	680	680	Contig1	2551648	2407622	2408697	8	4,342,14,13,24,14,120,146,	0,4,346,361,374,399,414,534,	2407622,2407627,2408361,2408375,2408389,2408416,2408430,2408551,
587	674	6	0	0	0	0	0	+	EH380974	680	680	Contig10	1061368	321851	322531	1	680,	0,	321851,

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