Schema for refSeqAli

Database: hg19 Primary Table: refSeqAli Row Count: 36,002
Format description: Summary info about a patSpace alignment

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	1731	`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`	37	`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`	10	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	13240	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	NR_024540	`varchar(255)`	values	Query sequence name
`qSize`	1786	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	1768	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	249250621	`int(10) unsigned`	range	Target sequence size
`tStart`	14362	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	29370	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	11	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	467,69,152,159,198,136,137,...	`longblob`		Size of each block
`qStarts`	18,485,554,706,865,1063,119...	`longblob`		Start of each block in query.
`tStarts`	14362,14969,15795,16606,168...	`longblob`		Start of each block in target.

      hg19.all_est.qName (via refSeqAli.qName)
      hg19.all_mrna.qName (via refSeqAli.qName)
      hg19.ccdsInfo.mrnaAcc (via refSeqAli.qName)
      hg19.gbCdnaInfo.acc (via refSeqAli.qName)
      hg19.gbMiscDiff.acc (via refSeqAli.qName)
      hg19.gbSeq.acc (via refSeqAli.qName)
      hg19.gbStatus.acc (via refSeqAli.qName)
      hg19.gbWarn.acc (via refSeqAli.qName)
      hg19.imageClone.acc (via refSeqAli.qName)
      hg19.kgXref.refseq (via refSeqAli.qName)
      hg19.knownToRefSeq.value (via refSeqAli.qName)
      hg19.mrnaOrientInfo.name (via refSeqAli.qName)
      hg19.refFlat.name (via refSeqAli.qName)
      hg19.refGene.name (via refSeqAli.qName)
      hg19.refLink.mrnaAcc (via refSeqAli.qName)
      hg19.refSeqStatus.mrnaAcc (via refSeqAli.qName)
      hg19.refSeqSummary.mrnaAcc (via refSeqAli.qName)
      hg19.seq.acc (via refSeqAli.qName)
      hg19.xenoMrna.qName (via refSeqAli.qName)
      hg19.xenoRefGene.name (via refSeqAli.qName)
      hg19.xenoRefSeqAli.qName (via refSeqAli.qName)

bin	matches	repMatches	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	1731	37	10	13240	-	NR_024540	1786	1768	chr1	249250621	14362	29370	11	467,69,152,159,198,136,137,147,99,154,50,	18,485,554,706,865,1063,1199,1336,1483,1582,1736,	14362,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,
585	918	0	0	0	+	NM_001005484	918	918	chr1	249250621	69090	70008	1	918,	0,	69090,
587	937	0	0	0	+	NM_001005221	939	937	chr1	249250621	367658	368595	1	937,	0,	367658,
587	937	0	0	0	+	NM_001005224	939	937	chr1	249250621	367658	368595	1	937,	0,	367658,
587	937	0	0	0	+	NM_001005277	939	937	chr1	249250621	367658	368595	1	937,	0,	367658,
589	937	0	0	0	-	NM_001005221	939	937	chr1	249250621	621097	622034	1	937,	2,	621097,
589	937	0	0	0	-	NM_001005224	939	937	chr1	249250621	621097	622034	1	937,	2,	621097,
589	937	0	0	0	-	NM_001005277	939	937	chr1	249250621	621097	622034	1	937,	2,	621097,
590	1316	0	0	0	-	NR_024321	1317	1316	chr1	249250621	761586	762902	1	1316,	1,	761586,
73	1396	147	6	25134	+	NR_015368	1543	1543	chr1	249250621	763063	789740	7	92,102,153,184,96,132,784,	0,92,194,347,531,627,759,	763063,764382,783033,787306,788050,788770,788956,

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