Schema for all

Schema for all_est

Database: ailMel1 Primary Table: all_est Row Count: 2 Data last updated: 2018-04-23
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	604	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	346	`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`	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`	AF325534	`varchar(255)`	values	Query sequence name
`qSize`	374	`int(10) unsigned`	range	Query sequence size
`qStart`	14	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	361	`int(10) unsigned`	range	Alignment end position in query
`tName`	GL192437.1	`varchar(255)`	values	Target sequence name
`tSize`	2818556	`int(10) unsigned`	range	Target sequence size
`tStart`	2583395	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	2583743	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	152,195,	`longblob`		Size of each block
`qStarts`	13,165,	`longblob`		Start of each block in query.
`tStarts`	2583395,2583548,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	ailMel1.all_mrna.qName (via all_est.qName) ailMel1.estOrientInfo.name (via all_est.qName) ailMel1.xenoMrna.qName (via all_est.qName) ailMel1.xenoRefGene.name (via all_est.qName) ailMel1.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	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
604	346	1	0	0	0	0	1	1	-	AF325534	374	14	361	GL192437.1	2818556	2583395	2583743	2	152,195,	13,165,	2583395,2583548,
588	561	4	0	0	0	0	1	176	-	AF325709	572	0	565	GL192735.1	1530502	425134	425875	2	558,7,	7,565,	425134,425868,

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