Schema for all

Schema for all_mrna

Database: criGriChoV1 Primary Table: all_mrna Row Count: 70,110 Data last updated: 2018-11-01
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	590	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	684	`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`	1	`int(10) unsigned`	range	Number of 'N' bases
`qNumInsert`	2	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	2	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	2	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	936	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	JI870364	`varchar(255)`	values	Query sequence name
`qSize`	687	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	687	`int(10) unsigned`	range	Alignment end position in query
`tName`	NW_003613580v1	`varchar(255)`	values	Target sequence name
`tSize`	8779783	`int(10) unsigned`	range	Target sequence size
`tStart`	736931	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	738552	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	5	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	175,372,37,22,79,	`longblob`		Size of each block
`qStarts`	0,175,547,585,608,	`longblob`		Start of each block in query.
`tStarts`	736931,738041,738414,738451...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	criGriChoV1.all_est.qName (via all_mrna.qName) criGriChoV1.mrnaOrientInfo.name (via all_mrna.qName) criGriChoV1.refGene.name (via all_mrna.qName) criGriChoV1.refSeqAli.qName (via all_mrna.qName) criGriChoV1.xenoRefGene.name (via all_mrna.qName) criGriChoV1.xenoRefSeqAli.qName (via all_mrna.qName) 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)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
590	684	0	1	2	2	2	936	+	JI870364	687	687	NW_003613580v1	8779783	736931	738552	5	175,372,37,22,79,	0,175,547,585,608,	736931,738041,738414,738451,738473,
590	684	0	1	2	2	2	936	+	JP052302	687	687	NW_003613580v1	8779783	736931	738552	5	175,372,37,22,79,	0,175,547,585,608,	736931,738041,738414,738451,738473,
590	584	0	0	0	0	0	0	+	JI874075	584	584	NW_003613580v1	8779783	739307	739891	1	584,	0,	739307,
590	556	0	0	0	0	0	0	+	JP061733	556	556	NW_003613580v1	8779783	739335	739891	1	556,	0,	739335,
74	542	0	0	1	1	0	0	-	JI890891	543	543	NW_003613580v1	8779783	1834570	1835112	2	365,177,	0,366,	1834570,1834935,
74	542	0	0	1	1	0	0	-	JP040089	543	543	NW_003613580v1	8779783	1834570	1835112	2	365,177,	0,366,	1834570,1834935,
599	506	0	0	1	1	0	0	-	JI873173	507	507	NW_003613580v1	8779783	1835350	1835856	2	4,502,	0,5,	1835350,1835354,
599	506	0	0	0	0	0	0	-	JP047769	506	506	NW_003613580v1	8779783	1835350	1835856	1	506,	0,	1835350,
599	343	2	0	4	5	2	387	-	JI869765	350	350	NW_003613580v1	8779783	1855213	1855945	7	11,7,8,6,89,125,99,	0,13,21,30,37,126,251,	1855213,1855224,1855231,1855239,1855245,1855720,1855846,
599	343	2	0	3	4	2	387	-	JP059056	349	349	NW_003613580v1	8779783	1855213	1855945	6	10,16,6,89,125,99,	0,12,29,36,125,250,	1855213,1855223,1855239,1855245,1855720,1855846,

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