Schema for all

Schema for all_est

Database: sacCer3 Primary Table: all_est Row Count: 34,991 Data last updated: 2012-05-25
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`	442	`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`	9	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	25	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	3	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	15	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	AA417479	`varchar(255)`	values	Query sequence name
`qSize`	472	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	472	`int(10) unsigned`	range	Alignment end position in query
`tName`	chrI	`varchar(255)`	values	Target sequence name
`tSize`	230218	`int(10) unsigned`	range	Target sequence size
`tStart`	51171	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	51633	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	11	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	14,5,4,12,16,8,13,15,11,20,...	`longblob`		Size of each block
`qStarts`	0,23,29,34,54,71,80,94,110,...	`longblob`		Start of each block in query.
`tStarts`	51171,51193,51198,51202,512...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	hgFixed.gbCdnaInfo.acc (via all_est.qName) hgFixed.gbMiscDiff.acc (via all_est.qName) hgFixed.gbSeq.acc (via all_est.qName) hgFixed.gbWarn.acc (via all_est.qName) hgFixed.imageClone.acc (via all_est.qName) sacCer3.all_mrna.qName (via all_est.qName) sacCer3.est.qName (via all_est.qName) sacCer3.estOrientInfo.name (via all_est.qName) sacCer3.intronEst.qName (via all_est.qName) sacCer3.xenoRefGene.name (via all_est.qName) sacCer3.xenoRefSeqAli.qName (via all_est.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	442	5	0	9	25	3	15	-	AA417479	472	0	472	chrI	230218	51171	51633	11	14,5,4,12,16,8,13,15,11,20,329,	0,23,29,34,54,71,80,94,110,123,143,	51171,51193,51198,51202,51220,51236,51244,51257,51272,51283,51304,
586	457	1	0	7	14	3	5	-	AA417480	472	0	472	chrI	230218	146592	147055	8	5,4,10,8,10,20,40,361,	0,6,11,25,34,46,70,111,	146592,146597,146601,146613,146621,146632,146654,146694,
586	381	0	1	1	1	2	4	+	AA417481	390	7	390	chrI	230218	160868	161254	3	24,342,16,	7,32,374,	160868,160895,161238,
586	279	5	3	0	0	0	0	-	AA417477	287	0	287	chrI	230218	187940	188227	1	287,	0,	187940,
587	450	0	0	0	0	0	0	-	AA417529	450	0	450	chrII	813184	315422	315872	1	450,	0,	315422,
587	347	1	0	1	2	1	1	-	AA417450	350	0	350	chrII	813184	382322	382671	2	46,302,	0,48,	382322,382369,
588	54	0	0	0	0	0	0	+	AA417466	54	0	54	chrII	813184	492467	492521	1	54,	0,	492467,
590	77	0	0	0	0	0	0	-	AA417449	77	0	77	chrII	813184	731444	731521	1	77,	0,	731444,
590	325	1	2	2	2	0	0	+	AA417475	336	0	330	chrII	813184	768593	768921	3	298,10,20,	0,299,310,	768593,768891,768901,
586	448	0	0	2	2	0	0	-	AA417448	450	0	450	chrIII	316620	138321	138769	3	44,69,335,	0,45,115,	138321,138365,138434,

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