Schema for all

Schema for all_est

Database: calMil1 Primary Table: all_est Row Count: 122,904 Data last updated: 2016-04-10
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`	508	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	3	`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`	JK860342	`varchar(255)`	values	Query sequence name
`qSize`	511	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	511	`int(10) unsigned`	range	Alignment end position in query
`tName`	AAVX02039917	`varchar(255)`	values	Target sequence name
`tSize`	81585	`int(10) unsigned`	range	Target sequence size
`tStart`	79940	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	80451	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	1	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	511,	`longblob`		Size of each block
`qStarts`	0,	`longblob`		Start of each block in query.
`tStarts`	79940,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	calMil1.all_mrna.qName (via all_est.qName) calMil1.estOrientInfo.name (via all_est.qName) calMil1.intronEst.qName (via all_est.qName) calMil1.xenoRefGene.name (via all_est.qName) calMil1.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	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	508	3	0	0	-	JK860342	511	0	511	AAVX02039917	81585	79940	80451	1	511,	0,	79940,
585	644	1	2	2134	+	JK953043	645	0	645	AAVX02040487	63407	51985	54764	3	90,104,451,	0,90,194,	51985,53721,54313,
585	647	2	2	2134	+	JK962816	649	0	649	AAVX02040487	63407	52034	54817	3	41,104,504,	0,41,145,	52034,53721,54313,
585	574	0	0	0	+	JK873452	574	0	574	AAVX02040487	63407	54540	55114	1	574,	0,	54540,
585	671	2	0	0	+	JK923722	673	0	673	AAVX02040487	63407	55608	56281	1	673,	0,	55608,
585	616	4	0	0	+	JK910813	620	0	620	AAVX02040487	63407	55661	56281	1	620,	0,	55661,
585	665	3	0	0	-	JK948054	685	0	668	AAVX02041197	47682	26026	26694	1	668,	17,	26026,
585	758	4	0	0	-	JK949151	779	1	763	AAVX02041197	47682	26026	26788	1	762,	16,	26026,
585	658	4	0	0	-	JK948156	678	0	662	AAVX02041197	47682	26027	26689	1	662,	16,	26027,
585	706	5	0	0	-	JK947659	727	0	711	AAVX02041197	47682	26027	26738	1	711,	16,	26027,

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