Schema for all

Schema for all_est

Database: anoGam3 Primary Table: all_est Row Count: 151,395 Data last updated: 2018-01-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	664	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	565	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	9	`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`	3	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	11	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	5	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	155	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	+	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AA413325	`varchar(255)`	values	Query sequence name
`qSize`	590	`int(10) unsigned`	range	Query sequence size
`qStart`	5	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	590	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr2L	`varchar(255)`	values	Target sequence name
`tSize`	49364325	`int(10) unsigned`	range	Target sequence size
`tStart`	10356718	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	10357447	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	8	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	169,22,53,218,37,37,33,5,	`longblob`		Size of each block
`qStarts`	5,183,205,258,477,514,551,585,	`longblob`		Start of each block in query.
`tStarts`	10356718,10356898,10357061,...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	anoGam3.all_mrna.qName (via all_est.qName) anoGam3.estOrientInfo.name (via all_est.qName) anoGam3.intronEst.qName (via all_est.qName) anoGam3.xenoMrna.qName (via all_est.qName) anoGam3.xenoRefGene.name (via all_est.qName) anoGam3.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	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
664	565	9	3	11	5	155	+	AA413325	590	5	590	chr2L	49364325	10356718	10357447	8	169,22,53,218,37,37,33,5,	5,183,205,258,477,514,551,585,	10356718,10356898,10357061,10357115,10357333,10357371,10357409,10357442,
664	448	1	0	0	1	1	-	AA413326	492	43	492	chr2L	49364325	10358152	10358602	2	408,41,	0,408,	10358152,10358561,
714	482	7	5	9	4	9	-	AA413327	575	52	550	chr2L	49364325	17000030	17000528	8	165,55,29,16,61,143,11,9,	25,190,246,276,297,359,502,514,	17000030,17000196,17000251,17000280,17000299,17000360,17000504,17000519,
714	565	12	3	18	9	1290	-	AA413348	635	20	615	chr2L	49364325	17002880	17004747	11	5,4,27,14,57,24,9,55,60,262,60,	20,25,29,56,79,136,167,176,233,293,555,	17002880,17002887,17002892,17002920,17002950,17003008,17003044,17003054,17003109,17003170,17004687,
775	398	2	0	0	1	1	-	AA413350	417	17	417	chr2L	49364325	25016757	25017158	2	184,216,	0,184,	25016757,25016942,
779	570	4	6	22	11	45	+	AA413349	623	24	620	chr2L	49364325	25521648	25522267	14	44,63,28,107,7,241,6,3,26,20,4,8,9,8,	24,68,131,160,269,276,517,523,526,557,577,587,599,612,	25521648,25521693,25521757,25521785,25521892,25521900,25522142,25522149,25522153,25522189,25522210,25522225,25522240,25522259,
798	242	2	3	20	6	16	+	AA413351	285	17	281	chr2L	49364325	27928098	27928358	8	35,75,57,26,21,15,8,7,	17,55,138,195,221,242,266,274,	27928098,27928133,27928212,27928270,27928297,27928321,27928342,27928351,
831	633	2	1	6	11	2706	+	AA413352	660	19	660	chr2L	49364325	32370994	32374335	12	84,187,64,158,34,34,3,30,13,11,7,10,	19,103,290,354,512,546,580,583,613,626,637,650,	32370994,32371092,32371280,32373272,32374176,32374211,32374246,32374250,32374281,32374295,32374308,32374325,
832	511	13	1	1	5	18	+	AA413353	547	0	525	chr2L	49364325	32375087	32375629	7	30,45,30,171,34,185,29,	0,30,75,106,277,311,496,	32375087,32375122,32375168,32375198,32375379,32375414,32375600,
868	283	0	0	0	4	79	+	AA413354	300	17	300	chr2L	49364325	37127399	37127761	5	41,7,195,26,14,	17,58,65,260,286,	37127399,37127516,37127524,37127720,37127747,

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