Schema for all

Schema for all_mrna

Database: canFam1 Primary Table: all_mrna Row Count: 3,859 Data last updated: 2020-08-21
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	630	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	4109	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	111	`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`	6	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	6	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AB012223	`varchar(255)`	values	Query sequence name
`qSize`	4251	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	4220	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	124897793	`int(10) unsigned`	range	Target sequence size
`tStart`	5974522	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	5978748	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	7	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	226,1001,77,1124,750,669,373,	`longblob`		Size of each block
`qStarts`	31,257,1258,1335,2459,3209,...	`longblob`		Start of each block in query.
`tStarts`	5974522,5974749,5975751,597...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	canFam1.all_est.qName (via all_mrna.qName) canFam1.mrnaOrientInfo.name (via all_mrna.qName) canFam1.refGene.name (via all_mrna.qName) canFam1.refSeqAli.qName (via all_mrna.qName) canFam1.xenoMrna.qName (via all_mrna.qName) canFam1.xenoRefGene.name (via all_mrna.qName) canFam1.xenoRefSeqAli.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	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
630	4109	111	0	0	6	6	-	AB012223	4251	0	4220	chr1	124897793	5974522	5978748	7	226,1001,77,1124,750,669,373,	31,257,1258,1335,2459,3209,3878,	5974522,5974749,5975751,5975829,5976954,5977705,5978375,
645	460	0	0	0	4	35293	+	HM154531	460	0	460	chr1	124897793	7943221	7978974	5	161,129,30,35,105,	0,161,290,320,355,	7943221,7971092,7973074,7977128,7978869,
10	4099	106	0	0	9	612332	-	AB012223	4251	0	4205	chr1	124897793	9083878	9700415	10	182,749,848,17,423,262,220,19,901,584,	46,228,977,1825,1842,2265,2527,2747,2766,3667,	9083878,9327836,9697132,9697981,9697999,9698424,9698687,9698908,9698929,9699831,
83	4117	100	1	3	1	289587	+	AB012223	4251	0	4220	chr1	124897793	10490608	10784412	3	3224,791,202,	0,3227,4018,	10490608,10493832,10784210,
669	4099	109	0	0	0	0	-	AB012223	4251	0	4208	chr1	124897793	11032719	11036927	1	4208,	43,	11032719,
705	4109	110	1	1	4	5	-	AB012223	4251	0	4220	chr1	124897793	15739801	15744025	5	357,378,1647,622,1215,	31,389,767,2414,3036,	15739801,15740160,15740539,15742187,15742810,
1	1245	6	3	104	3	165513	+	AB154172	1374	0	1355	chr1	124897793	16624492	16791256	6	88,59,209,229,328,338,	0,90,149,359,689,1017,	16624492,16624580,16624865,16625074,16625364,16790918,
1	578	29	1	104	2	165299	+	AY509563	711	0	711	chr1	124897793	16625147	16791053	3	145,327,135,	0,249,576,	16625147,16625365,16790918,
1	664	2	0	0	1	165226	+	AB116145	686	1	667	chr1	124897793	16625364	16791256	2	328,338,	1,329,	16625364,16790918,
1	392	25	2	27	3	165253	+	KC152952	462	18	462	chr1	124897793	16625383	16791053	4	49,44,189,135,	18,72,138,327,	16625383,16625437,16625503,16790918,

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