Schema for xenoMrna

Database: ci1 Primary Table: xenoMrna Row Count: 3,031,526 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	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`matches`	227	`int(10) unsigned`	Number of bases that match that aren't repeats
`misMatches`	85	`int(10) unsigned`	Number of bases that don't match
`repMatches`	0	`int(10) unsigned`	Number of bases that match but are part of repeats
`nCount`	0	`int(10) unsigned`	Number of 'N' bases
`qNumInsert`	1	`int(10) unsigned`	Number of inserts in query
`qBaseInsert`	393	`int(10) unsigned`	Number of bases inserted in query
`tNumInsert`	2	`int(10) unsigned`	Number of inserts in target
`tBaseInsert`	2975	`int(10) unsigned`	Number of bases inserted in target
`strand`	++	`char(2)`	+ or - for strand. First character query, second target (optional)
`qName`	AB179031	`varchar(255)`	Query sequence name
`qSize`	2227	`int(10) unsigned`	Query sequence size
`qStart`	1223	`int(10) unsigned`	Alignment start position in query
`qEnd`	1928	`int(10) unsigned`	Alignment end position in query
`tName`	Scaffold_1	`varchar(255)`	Target sequence name
`tSize`	972361	`int(10) unsigned`	Target sequence size
`tStart`	547	`int(10) unsigned`	Alignment start position in target
`tEnd`	3834	`int(10) unsigned`	Alignment end position in target
`blockCount`	3	`int(10) unsigned`	Number of blocks in alignment
`blockSizes`	69,99,144,	`longblob`	Size of each block
`qStarts`	1223,1685,1784,	`longblob`	Start of each block in query.
`tStarts`	547,3169,3690,	`longblob`	Start of each block in target.

Connected Tables and Joining Fields


	ci1.all_est.qName (via xenoMrna.qName) ci1.all_mrna.qName (via xenoMrna.qName) ci1.refGene.name (via xenoMrna.qName) ci1.refSeqAli.qName (via xenoMrna.qName) ci1.xenoRefFlat.name (via xenoMrna.qName) ci1.xenoRefGene.name (via xenoMrna.qName) ci1.xenoRefSeqAli.qName (via xenoMrna.qName) hgFixed.gbCdnaInfo.acc (via xenoMrna.qName) hgFixed.gbMiscDiff.acc (via xenoMrna.qName) hgFixed.gbSeq.acc (via xenoMrna.qName) hgFixed.gbWarn.acc (via xenoMrna.qName) hgFixed.imageClone.acc (via xenoMrna.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	227	85	1	393	2	2975	++	AB179031	2227	1223	1928	Scaffold_1	972361	547	3834	3	69,99,144,	1223,1685,1784,	547,3169,3690,
585	256	98	1	393	2	2975	++	AK308846	2855	1648	2395	Scaffold_1	972361	547	3876	3	69,99,186,	1648,2110,2209,	547,3169,3690,
585	256	98	1	393	2	2975	++	AK311044	2835	1581	2328	Scaffold_1	972361	547	3876	3	69,99,186,	1581,2043,2142,	547,3169,3690,
585	281	127	2	507	3	3343	++	AK172901	5139	1274	2189	Scaffold_1	972361	547	4298	4	69,99,186,54,	1274,1742,1841,2135,	547,3169,3690,4244,
585	285	124	2	497	3	3342	++	BC149377	5063	1847	2753	Scaffold_1	972361	547	4298	4	69,100,186,54,	1847,2305,2405,2699,	547,3168,3690,4244,
585	288	120	2	501	3	3343	++	D73409	6207	1763	2672	Scaffold_1	972361	547	4298	4	69,99,186,54,	1763,2225,2324,2618,	547,3169,3690,4244,
585	294	114	2	501	3	3343	++	AB078966	6281	1827	2736	Scaffold_1	972361	547	4298	4	69,99,186,54,	1827,2289,2388,2682,	547,3169,3690,4244,
585	294	114	2	501	3	3343	++	D63479	6238	1768	2677	Scaffold_1	972361	547	4298	4	69,99,186,54,	1768,2230,2329,2623,	547,3169,3690,4244,
585	294	114	2	609	3	3343	++	BC032102	5396	797	1814	Scaffold_1	972361	547	4298	4	69,99,186,54,	797,1367,1466,1760,	547,3169,3690,4244,
585	295	113	2	501	3	3343	++	AK307426	1939	385	1294	Scaffold_1	972361	547	4298	4	69,99,186,54,	385,847,946,1240,	547,3169,3690,4244,

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