Schema for all

Schema for all_mrna

Database: rn3 Primary Table: all_mrna Row Count: 126,150 Data last updated: 2020-08-23
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`	30	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	0	`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`	0	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	DQ763579	`varchar(255)`	values	Query sequence name
`qSize`	30	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	30	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	268121971	`int(10) unsigned`	range	Target sequence size
`tStart`	29100	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	29130	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	30,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	29100,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via all_mrna.qName) hgFixed.gbMiscDiff.acc (via all_mrna.qName) hgFixed.gbSeq.acc (via all_mrna.qName) hgFixed.gbWarn.acc (via all_mrna.qName) hgFixed.imageClone.acc (via all_mrna.qName) rn3.all_est.qName (via all_mrna.qName) rn3.dupSpMrna.dupMrnaID (via all_mrna.qName) rn3.dupSpMrna.mrnaID (via all_mrna.qName) rn3.mgcFullMrna.qName (via all_mrna.qName) rn3.mgcGenes.name (via all_mrna.qName) rn3.mrnaOrientInfo.name (via all_mrna.qName) rn3.mrnaRefseq.mrna (via all_mrna.qName) rn3.refGene.name (via all_mrna.qName) rn3.refSeqAli.qName (via all_mrna.qName) rn3.spMrna.mrnaID (via all_mrna.qName) rn3.xenoMrna.qName (via all_mrna.qName) rn3.xenoRefGene.name (via all_mrna.qName) rn3.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows

bin	matches	misMatches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	30	0	+	DQ763579	30	30	chr1	268121971	29100	29130	1	30,	0,	29100,
585	30	0	+	DQ763579	30	30	chr1	268121971	41645	41675	1	30,	0,	41645,
585	260	1	-	DQ255910	261	261	chr1	268121971	128612	128873	1	261,	0,	128612,
586	30	0	-	DQ763579	30	30	chr1	268121971	226886	226916	1	30,	0,	226886,
586	30	0	-	DQ763579	30	30	chr1	268121971	228276	228306	1	30,	0,	228276,
586	669	9	+	FQ226869	694	678	chr1	268121971	234634	235312	1	678,	0,	234634,
586	674	4	+	FQ232372	695	678	chr1	268121971	234634	235312	1	678,	0,	234634,
587	30	0	-	DQ742249	30	30	chr1	268121971	387210	387240	1	30,	0,	387210,
589	30	0	+	DQ617979	30	30	chr1	268121971	551903	551933	1	30,	0,	551903,
589	87	0	-	U25478	113	87	chr1	268121971	556699	556786	1	87,	26,	556699,

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