Schema for all

Schema for all_mrna

Database: micMur1 Primary Table: all_mrna Row Count: 160 Data last updated: 2017-07-04
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`	102	`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`	FJ869064	`varchar(255)`	values	Query sequence name
`qSize`	744	`int(10) unsigned`	range	Query sequence size
`qStart`	505	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	607	`int(10) unsigned`	range	Alignment end position in query
`tName`	scaffold_102452	`varchar(255)`	values	Target sequence name
`tSize`	1633	`int(10) unsigned`	range	Target sequence size
`tStart`	198	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	300	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	102,	`longblob`		Size of each block
`qStarts`	137,	`longblob`		Start of each block in query.
`tStarts`	198,	`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) micMur1.mrnaOrientInfo.name (via all_mrna.qName) micMur1.xenoRefGene.name (via all_mrna.qName) micMur1.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows

bin	matches	misMatches	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	102	0	-	FJ869064	744	505	607	scaffold_102452	1633	198	300	1	102,	137,	198,
585	99	3	-	FJ869065	744	505	607	scaffold_102452	1633	198	300	1	102,	137,	198,
585	100	2	-	FJ869066	744	505	607	scaffold_102452	1633	198	300	1	102,	137,	198,
585	99	3	-	FJ869067	744	505	607	scaffold_102452	1633	198	300	1	102,	137,	198,
585	98	4	-	FJ869068	753	515	617	scaffold_102452	1633	198	300	1	102,	136,	198,
585	98	4	-	FJ869069	753	515	617	scaffold_102452	1633	198	300	1	102,	136,	198,
585	101	1	-	FJ869070	753	515	617	scaffold_102452	1633	198	300	1	102,	136,	198,
585	110	2	+	HQ222943	867	755	867	scaffold_10562	42047	40491	40603	1	112,	755,	40491,
585	109	3	+	HQ222944	867	755	867	scaffold_10562	42047	40491	40603	1	112,	755,	40491,
585	108	4	+	HQ222945	867	755	867	scaffold_10562	42047	40491	40603	1	112,	755,	40491,

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