Schema for all

Schema for all_mrna

Database: rn7 Primary Table: all_mrna Row Count: 248,138 Data last updated: 2021-03-24
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`	24	`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`	DQ747939	`varchar(255)`	values	Query sequence name
`qSize`	24	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	24	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	260522016	`int(10) unsigned`	range	Target sequence size
`tStart`	6252	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	6276	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	24,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	6252,	`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) rn7.all_est.qName (via all_mrna.qName) rn7.mgcFullMrna.qName (via all_mrna.qName) rn7.mgcGenes.name (via all_mrna.qName) rn7.mrnaOrientInfo.name (via all_mrna.qName) rn7.refGene.name (via all_mrna.qName) rn7.refSeqAli.qName (via all_mrna.qName) rn7.xenoMrna.qName (via all_mrna.qName) rn7.xenoRefGene.name (via all_mrna.qName) rn7.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows

bin	matches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	24	-	DQ747939	24	24	chr1	260522016	6252	6276	1	24,	0,	6252,
585	30	+	DQ610247	30	30	chr1	260522016	14268	14298	1	30,	0,	14268,
585	29	+	DQ616750	29	29	chr1	260522016	14340	14369	1	29,	0,	14340,
585	26	+	DQ757846	27	26	chr1	260522016	23251	23277	1	26,	0,	23251,
585	26	+	DQ753126	26	26	chr1	260522016	28258	28284	1	26,	0,	28258,
585	30	-	DQ615682	31	30	chr1	260522016	43666	43696	1	30,	1,	43666,
585	26	-	DQ757846	27	26	chr1	260522016	47524	47550	1	26,	1,	47524,
585	24	+	DQ732226	24	24	chr1	260522016	61939	61963	1	24,	0,	61939,
585	24	+	DQ732226	24	24	chr1	260522016	112199	112223	1	24,	0,	112199,
585	25	+	DQ760294	25	25	chr1	260522016	127108	127133	1	25,	0,	127108,

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