Schema for refSeqAli

Database: ci3 Primary Table: refSeqAli Row Count: 1,304 Data last updated: 2017-04-10
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	587	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	1581	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	49	`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`	6	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	33	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	4	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	9	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	NM_001128115	`varchar(255)`	values	Query sequence name
`qSize`	1692	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	1663	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	10041005	`int(10) unsigned`	range	Target sequence size
`tStart`	343978	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	345617	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	9	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	216,72,5,25,60,133,15,149,955,	`longblob`		Size of each block
`qStarts`	29,265,337,343,369,429,563,...	`longblob`		Start of each block in query.
`tStarts`	343978,344197,344270,344275...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	ci3.all_est.qName (via refSeqAli.qName) ci3.all_mrna.qName (via refSeqAli.qName) ci3.mrnaOrientInfo.name (via refSeqAli.qName) ci3.refFlat.name (via refSeqAli.qName) ci3.refGene.name (via refSeqAli.qName) ci3.xenoRefGene.name (via refSeqAli.qName) ci3.xenoRefSeqAli.qName (via refSeqAli.qName) hgFixed.gbCdnaInfo.acc (via refSeqAli.qName) hgFixed.gbMiscDiff.acc (via refSeqAli.qName) hgFixed.gbSeq.acc (via refSeqAli.qName) hgFixed.gbWarn.acc (via refSeqAli.qName) hgFixed.imageClone.acc (via refSeqAli.qName) hgFixed.refLink.mrnaAcc (via refSeqAli.qName) hgFixed.refSeqStatus.mrnaAcc (via refSeqAli.qName) hgFixed.refSeqSummary.mrnaAcc (via refSeqAli.qName) knownGeneV39.kgXref.refseq (via refSeqAli.qName) knownGeneV39.knownToRefSeq.value (via refSeqAli.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
587	1581	49	6	33	4	9	-	NM_001128115	1692	0	1663	chr1	10041005	343978	345617	9	216,72,5,25,60,133,15,149,955,	29,265,337,343,369,429,563,582,737,	343978,344197,344270,344275,344300,344364,344497,344513,344662,
589	3538	20	0	0	7	3927	-	NM_001245043	3564	0	3558	chr1	10041005	540182	547667	8	1554,228,232,976,203,143,144,78,	6,1560,1788,2020,2996,3199,3342,3486,	540182,542094,542594,543125,544450,545757,546322,547589,
590	1139	11	1	2	3	679	-	NM_001078521	1183	0	1152	chr1	10041005	682412	684241	5	279,612,91,96,72,	31,312,924,1015,1111,	682412,682691,683591,683784,684169,
591	2173	11	0	0	3	7825	+	NM_001078308	2200	0	2184	chr1	10041005	824044	834053	4	590,204,167,1223,	0,590,794,961,	824044,831619,832492,832830,
591	709	2	0	0	10	5791	-	NM_001033838	711	0	711	chr1	10041005	838367	844869	11	168,42,135,41,40,21,42,47,37,95,43,	0,168,210,345,386,426,447,489,536,573,668,	838367,838707,839045,839542,840036,840252,840821,841208,842017,843027,844826,
591	2139	23	1	1	4	4	-	NM_001128901	2175	11	2174	chr1	10041005	891041	893207	6	50,27,1146,25,49,865,	1,52,79,1225,1250,1299,	891041,891091,891119,892266,892292,892342,
73	1997	0	0	0	17	4363	-	NM_001128903	1998	0	1997	chr1	10041005	916400	922760	18	62,166,49,71,110,146,201,111,112,176,145,80,118,73,37,92,67,181,	1,63,229,278,349,459,605,806,917,1029,1205,1350,1430,1548,1621,1658,1750,1817,	916400,916672,917057,917165,917335,917689,918084,918499,918877,919389,919915,920405,920802,921253,921381,921591,921990,922579,
592	53	0	0	0	0	0	+	NR_034561	53	0	53	chr1	10041005	919766	919819	1	53,	0,	919766,
592	3668	38	0	0	21	15217	+	NM_001128105	3725	0	3706	chr1	10041005	980135	999058	22	211,62,158,121,114,175,105,156,109,145,82,206,331,126,233,219,150,188,153,344,95,223,	0,211,273,431,552,666,841,946,1102,1211,1356,1438,1644,1975,2101,2334,2553,2703,2891,3044,3388,3483,	980135,980451,982044,982490,983001,983601,984487,989959,991941,992429,992870,993637,994326,995039,995520,996051,996805,997261,99 ...
592	53	0	0	0	0	0	+	NR_034536	53	0	53	chr1	10041005	1009503	1009556	1	53,	0,	1009503,

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