Schema for all

Schema for all_mrna

Database: fr2 Primary Table: all_mrna Row Count: 1,406 Data last updated: 2020-05-08
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	589	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	1168	`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`	23	`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`	8	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	3263	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB179548	`varchar(255)`	values	Query sequence name
`qSize`	1191	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	1191	`int(10) unsigned`	range	Alignment end position in query
`tName`	chrUn	`varchar(255)`	values	Target sequence name
`tSize`	400509343	`int(10) unsigned`	range	Target sequence size
`tStart`	617689	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	622143	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	9	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	162,99,145,123,200,119,124,...	`longblob`		Size of each block
`qStarts`	0,162,261,406,529,729,848,9...	`longblob`		Start of each block in query.
`tStarts`	617689,618023,618262,618477...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	fr2.all_est.qName (via all_mrna.qName) fr2.mrnaOrientInfo.name (via all_mrna.qName) fr2.xenoMrna.qName (via all_mrna.qName) 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)

Sample Rows

bin	matches	misMatches	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
589	1168	0	23	0	0	8	3263	-	AB179548	1191	0	1191	chrUn	400509343	617689	622143	9	162,99,145,123,200,119,124,157,62,	0,162,261,406,529,729,848,972,1129,	617689,618023,618262,618477,618822,619420,619616,620319,622081,
591	954	7	94	1	1	8	810	+	AB256950	1078	22	1078	chrUn	400509343	876958	878823	10	63,31,57,132,121,179,82,125,49,216,	22,85,116,173,305,426,605,687,812,862,	876958,877125,877239,877418,877656,877918,878184,878344,878558,878607,
592	710	1	32	0	0	2	721	-	DQ413000	792	49	792	chrUn	400509343	961599	963063	3	167,76,500,	0,167,243,	961599,962110,962563,
593	1225	0	152	0	0	1	444	-	EF371366	1377	0	1377	chrUn	400509343	1096798	1098619	2	1197,180,	0,1197,	1096798,1098439,
603	519	0	0	0	0	2	417	-	LC129229	547	3	522	chrUn	400509343	2448196	2449132	3	254,213,52,	25,279,492,	2448196,2448558,2449080,
604	1368	1	56	0	0	9	3357	+	AY298751	1425	0	1425	chrUn	400509343	2527117	2531899	10	138,45,110,80,168,195,87,30,80,492,	0,138,183,293,373,541,736,823,853,933,	2527117,2527373,2527921,2528433,2528943,2529173,2530725,2531031,2531062,2531407,
610	2272	1	76	0	0	19	15256	-	AB236415	2349	0	2349	chrUn	400509343	3287803	3305408	20	144,77,151,148,248,250,77,173,136,156,51,123,17,205,75,63,45,64,101,45,	0,144,221,372,520,768,1018,1095,1268,1404,1560,1611,1734,1751,1956,2031,2094,2139,2203,2304,	3287803,3288041,3288682,3288906,3289139,3289872,3290203,3290716,3290978,3292000,3292583,3292719,3294608,3295303,3298670,3298949, ...
612	1933	1	219	2	7	4	1465	+	AY529485	2177	0	2160	chrUn	400509343	3540684	3544302	7	88,121,131,138,171,952,552,	0,94,215,346,484,655,1608,	3540684,3540772,3541780,3542080,3542224,3542798,3543750,
615	1577	3	181	0	0	8	739	+	AB330136	1792	0	1761	chrUn	400509343	3961131	3963631	9	219,151,155,165,115,112,163,242,439,	0,219,370,525,690,805,917,1080,1322,	3961131,3961424,3961673,3961898,3962158,3962359,3962572,3962852,3963192,
616	1122	0	0	0	0	6	2324	+	HF936683	1122	0	1122	chrUn	400509343	4117127	4120573	7	81,119,97,340,126,140,219,	0,81,200,297,637,763,903,	4117127,4118295,4118629,4118921,4119512,4119731,4120354,

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