Schema for refSeqAli

Database: macFas5 Primary Table: refSeqAli Row Count: 2,163 Data last updated: 2019-12-05
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	74	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	1807	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	5	`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`	1	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	9	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	4	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	50291	`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_001283475	`varchar(255)`	values	Query sequence name
`qSize`	1924	`int(10) unsigned`	range	Query sequence size
`qStart`	3	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	1824	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr1	`varchar(255)`	values	Target sequence name
`tSize`	227556264	`int(10) unsigned`	range	Target sequence size
`tStart`	1699586	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	1751689	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	6	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	557,939,29,50,60,177,	`longblob`		Size of each block
`qStarts`	100,666,1605,1634,1684,1744,	`longblob`		Start of each block in query.
`tStarts`	1699586,1700143,1710585,171...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	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) macFas5.all_est.qName (via refSeqAli.qName) macFas5.all_mrna.qName (via refSeqAli.qName) macFas5.mrnaOrientInfo.name (via refSeqAli.qName) macFas5.refFlat.name (via refSeqAli.qName) macFas5.refGene.name (via refSeqAli.qName) macFas5.xenoRefGene.name (via refSeqAli.qName) macFas5.xenoRefSeqAli.qName (via refSeqAli.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
74	1807	5	0	1	9	4	50291	-	NM_001283475	1924	3	1824	chr1	227556264	1699586	1751689	6	557,939,29,50,60,177,	100,666,1605,1634,1684,1744,	1699586,1700143,1710585,1712907,1720103,1751512,
604	1722	7	0	2	104	10	51719	-	NM_001283331	1852	0	1833	chr1	227556264	2533456	2586904	12	198,414,82,112,57,120,118,131,50,132,113,202,	19,242,656,738,850,907,1027,1145,1276,1326,1537,1650,	2533456,2533654,2535100,2536550,2541801,2541964,2542904,2543622,2561797,2565509,2584375,2586702,
645	1597	7	0	0	0	9	20823	+	NM_001285175	1619	0	1604	chr1	227556264	7937257	7959684	10	160,135,111,177,183,166,204,128,154,186,	0,160,295,406,583,766,932,1136,1264,1418,	7937257,7939725,7943345,7945093,7948338,7950958,7952857,7954523,7956896,7959498,
673	1787	6	0	0	0	12	6309	+	NM_001285045	1810	0	1793	chr1	227556264	11583299	11591401	13	133,200,122,103,153,188,98,131,190,151,79,102,143,	0,133,333,455,558,711,899,997,1128,1318,1469,1548,1650,	11583299,11583433,11583893,11584100,11585546,11586495,11587188,11588170,11588477,11588738,11589202,11590968,11591258,
85	2933	19	31	0	0	7	178237	-	NM_001283135	2983	0	2983	chr1	227556264	12998900	13180120	8	2471,46,59,40,59,92,71,145,	0,2471,2517,2576,2616,2675,2767,2838,	12998900,13015501,13053806,13067307,13072789,13144875,13177810,13179975,
722	1857	2	0	0	0	5	37732	-	NM_001284818	2161	0	1859	chr1	227556264	17984466	18024057	6	1209,128,131,115,105,171,	302,1511,1639,1770,1885,1990,	17984466,17988841,18010481,18015735,18023349,18023886,
11	1821	12	0	1	1	5	9928	+	NM_001283634	1834	0	1834	chr1	227556264	18863134	18874895	7	36,859,268,145,263,111,151,	0,36,895,1163,1308,1572,1683,	18863134,18866358,18871017,18872883,18874365,18874628,18874744,
93	2070	5	0	0	0	6	54160	-	NM_001283325	2091	0	2075	chr1	227556264	21209160	21265395	7	349,1266,167,62,111,110,10,	16,365,1631,1798,1860,1971,2081,	21209160,21209515,21215793,21223306,21229670,21265274,21265385,
766	1284	2	0	0	0	6	39255	-	NM_001284144	1308	0	1286	chr1	227556264	23800085	23840626	7	680,145,68,47,60,78,208,	22,702,847,915,962,1022,1100,	23800085,23813872,23824538,23826309,23831501,23839926,23840418,
97	495	3	0	0	0	7	87676	-	NM_001283831	498	0	498	chr1	227556264	25397209	25485383	8	66,42,57,33,81,57,104,58,	0,66,108,165,198,279,336,440,	25397209,25398531,25399489,25400472,25403607,25404381,25405701,25485325,

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