Schema for all

Schema for all_est

Database: felCat4 Primary Table: all_est Row Count: 926 Data last updated: 2016-04-09
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	948	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	553	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	11	`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`	2	`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`	12	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	649	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AF034791	`varchar(255)`	values	Query sequence name
`qSize`	1367	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	566	`int(10) unsigned`	range	Alignment end position in query
`tName`	chrB4	`varchar(255)`	values	Target sequence name
`tSize`	164876586	`int(10) unsigned`	range	Target sequence size
`tStart`	47625337	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	47626552	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	13	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	23,107,84,6,116,82,47,38,19...	`longblob`		Size of each block
`qStarts`	0,23,130,214,220,336,418,46...	`longblob`		Start of each block in query.
`tStarts`	47625337,47625443,47625672,...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	felCat4.all_mrna.qName (via all_est.qName) felCat4.estOrientInfo.name (via all_est.qName) felCat4.intronEst.qName (via all_est.qName) felCat4.refGene.name (via all_est.qName) felCat4.refSeqAli.qName (via all_est.qName) felCat4.xenoMrna.qName (via all_est.qName) felCat4.xenoRefGene.name (via all_est.qName) felCat4.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	repMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
948	553	11	0	2	0	0	12	649	+	AF034791	1367	0	566	chrB4	164876586	47625337	47626552	13	23,107,84,6,116,82,47,38,19,4,16,7,17,	0,23,130,214,220,336,418,465,503,522,526,542,549,	47625337,47625443,47625672,47625757,47625872,47626090,47626398,47626446,47626485,47626505,47626510,47626527,47626535,
902	155	1	0	0	0	0	1	90	-	AF197970	891	0	156	chrX	145558876	41583008	41583254	2	89,67,	735,824,	41583008,41583187,
902	466	1	0	0	0	0	3	490	+	AF197970	891	153	620	chrX	145558876	41600066	41601023	4	160,213,28,66,	153,313,526,554,	41600066,41600376,41600927,41600957,
903	445	2	0	0	1	1	1	1	+	AF197969	459	0	448	chrX	145558876	41734252	41734700	3	155,268,24,	0,156,424,	41734252,41734407,41734676,
638	383	0	0	0	0	0	1	1	+	AW646939	383	0	383	chrA1	279330936	6999741	7000125	2	165,218,	0,165,	6999741,6999907,
666	427	3	0	3	2	2	3	3	-	AW646755	435	0	435	chrA1	279330936	10628377	10628813	6	16,264,35,47,33,38,	0,16,280,315,363,397,	10628377,10628394,10628659,10628695,10628742,10628775,
819	184	0	0	0	1	154	3	4428	+	AW646924	594	256	594	chrA1	279330936	30739689	30744301	4	110,25,29,20,	256,520,545,574,	30739689,30744225,30744251,30744281,
977	458	1	28	0	3	3	1	1	-	AW646754	490	0	490	chrA1	279330936	51384531	51385019	5	129,259,31,13,55,	0,129,389,421,435,	51384531,51384661,51384920,51384951,51384964,
1001	302	5	0	2	1	1	1	1	+	AW646753	311	0	310	chrA1	279330936	54624874	54625184	3	43,105,161,	0,44,149,	54624874,54624917,54625023,
1681	433	1	0	3	1	1	1	1	-	AW646764	438	0	438	chrA1	279330936	143727317	143727755	3	131,201,105,	0,131,333,	143727317,143727449,143727650,

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