Schema for all

Schema for all_mrna

Database: melGal5 Primary Table: all_mrna Row Count: 412 Data last updated: 2017-01-19
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	1208	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	4	`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`	4	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	507	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AM167974	`varchar(255)`	values	Query sequence name
`qSize`	1240	`int(10) unsigned`	range	Query sequence size
`qStart`	3	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	1215	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	190651702	`int(10) unsigned`	range	Target sequence size
`tStart`	123217	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	124936	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	5	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	502,155,266,198,91,	`longblob`		Size of each block
`qStarts`	25,527,682,948,1146,	`longblob`		Start of each block in query.
`tStarts`	123217,123802,124147,124573...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	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) melGal5.all_est.qName (via all_mrna.qName) melGal5.mrnaOrientInfo.name (via all_mrna.qName) melGal5.refGene.name (via all_mrna.qName) melGal5.refSeqAli.qName (via all_mrna.qName) melGal5.xenoRefGene.name (via all_mrna.qName) melGal5.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	1208	4	0	0	0	4	507	-	AM167974	1240	3	1215	chr1	190651702	123217	124936	5	502,155,266,198,91,	25,527,682,948,1146,	123217,123802,124147,124573,124845,
588	261	6	0	0	0	0	0	+	KC594105	267	0	267	chr1	190651702	491180	491447	1	267,	0,	491180,
644	2276	4	0	0	0	7	18465	+	KR528577	2280	0	2280	chr1	190651702	7735255	7756000	8	247,104,108,155,91,100,213,1262,	0,247,351,459,614,705,805,1018,	7735255,7738541,7742062,7743007,7743981,7747399,7749120,7754738,
733	4808	25	1	3	6	8	8813	+	KR528575	4848	1	4841	chr1	190651702	19482799	19496446	12	202,181,131,281,151,186,157,1944,601,595,376,29,	1,203,384,515,796,947,1133,1290,3237,3840,4435,4812,	19482799,19483820,19487632,19488165,19488760,19491423,19492123,19492900,19494844,19495445,19496041,19496417,
848	255	0	0	0	0	2	982	-	JQ280471	260	0	255	chr1	190651702	34525716	34526953	3	26,180,49,	5,31,211,	34525716,34526384,34526904,
851	215	5	0	0	0	2	1418	+	KC594103	220	0	220	chr1	190651702	34969495	34971133	3	93,77,50,	0,93,170,	34969495,34970047,34971083,
859	812	2	0	0	0	5	12089	+	DQ074976	824	10	824	chr1	190651702	35965726	35978629	6	153,184,101,68,197,111,	10,163,347,448,516,713,	35965726,35967437,35967727,35971222,35976685,35978518,
885	499	4	0	2	226	3	184	+	GU223068	729	0	729	chr1	190651702	39385517	39386204	5	237,8,23,111,124,	0,237,245,269,605,	39385517,39385755,39385764,39385787,39386080,
899	244	3	0	0	0	1	1595	+	KC594101	249	0	247	chr1	190651702	41249683	41251525	2	113,134,	0,113,	41249683,41251391,
949	392	1	1	0	0	3	2582	+	GQ281326	396	2	396	chr1	190651702	47744869	47747845	4	99,80,92,123,	2,101,181,273,	47744869,47745721,47746824,47747722,

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