Schema for all

Schema for all_est

Database: felCat9 Primary Table: all_est Row Count: 1,052 Data last updated: 2018-03-18
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	902	`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`	11	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	648	`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`	144528695	`int(10) unsigned`	range	Target sequence size
`tStart`	41632231	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	41633445	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	12	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	23,107,84,6,116,82,44,41,19...	`longblob`		Size of each block
`qStarts`	0,23,130,214,220,336,418,46...	`longblob`		Start of each block in query.
`tStarts`	41632231,41632337,41632566,...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	felCat9.all_mrna.qName (via all_est.qName) felCat9.estOrientInfo.name (via all_est.qName) felCat9.intronEst.qName (via all_est.qName) felCat9.refGene.name (via all_est.qName) felCat9.refSeqAli.qName (via all_est.qName) felCat9.xenoMrna.qName (via all_est.qName) felCat9.xenoRefGene.name (via all_est.qName) felCat9.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	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
902	553	11	2	0	0	11	648	+	AF034791	1367	0	566	chrB4	144528695	41632231	41633445	12	23,107,84,6,116,82,44,41,19,4,23,17,	0,23,130,214,220,336,418,462,503,522,526,549,	41632231,41632337,41632566,41632651,41632766,41632984,41633292,41633337,41633379,41633399,41633404,41633428,
864	882	3	0	0	0	7	6760	+	AF197970	891	0	885	chrX	130557009	36581476	36589121	8	67,89,157,213,28,66,245,20,	0,67,156,313,526,554,620,865,	36581476,36581633,36585267,36585574,36586124,36586154,36588563,36589101,
13	445	2	0	1	1	1	1	+	AF197969	459	0	448	chrX	130557009	36699842	36700290	3	155,268,24,	0,156,424,	36699842,36699997,36700266,
631	383	0	0	0	0	1	1	+	AW646939	383	0	383	chrA1	242100913	6083567	6083951	2	165,218,	0,165,	6083567,6083733,
654	427	3	3	2	2	3	3	-	AW646755	435	0	435	chrA1	242100913	9121422	9121858	6	16,264,35,47,33,38,	0,16,280,315,363,397,	9121422,9121439,9121704,9121740,9121787,9121820,
806	591	2	1	0	0	5	7994	+	AW646924	594	0	594	chrA1	242100913	29003270	29011858	6	65,65,126,110,155,73,	0,65,130,256,366,521,	29003270,29004278,29004773,29006053,29006991,29011785,
954	486	1	0	3	3	0	0	-	AW646754	490	0	490	chrA1	242100913	48377851	48378338	4	388,31,13,55,	0,389,421,435,	48377851,48378239,48378270,48378283,
976	304	4	2	1	1	1	1	+	AW646753	311	0	311	chrA1	242100913	51256318	51256629	3	43,105,162,	0,44,149,	51256318,51256361,51256467,
1230	505	1	2	0	0	5	4349	-	AW646766	508	0	508	chrA1	242100913	84618185	84623042	6	48,100,115,79,78,88,	0,48,148,263,342,420,	84618185,84618354,84621057,84622609,84622789,84622954,
1284	318	6	3	0	0	2	774	+	AW646765	328	1	328	chrA1	242100913	91639023	91640124	3	108,111,108,	1,109,220,	91639023,91639515,91640016,

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