Schema for affyGnf1h

Database: hg18 Primary Table: affyGnf1h Row Count: 12,084 Data last updated: 2006-02-01
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	792	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	496	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	1	`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`	0	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	0	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	1	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	713	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	gnf1h00031_at	`varchar(255)`	values	Query sequence name
`qSize`	497	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	497	`int(10) unsigned`	range	Alignment end position in query
`tName`	chr7	`varchar(255)`	values	Target sequence name
`tSize`	158821424	`int(10) unsigned`	range	Target sequence size
`tStart`	27204401	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	27205611	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	2	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	185,312,	`longblob`		Size of each block
`qStarts`	0,185,	`longblob`		Start of each block in query.
`tStarts`	27204401,27205299,	`longblob`		Start of each block in target.

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Connected Tables and Joining Fields


	hg18.gnfAtlas2.name (via affyGnf1h.qName) hg18.knownToGnfAtlas2.value (via affyGnf1h.qName) hgFixed.gladHumESOtherData.name (via affyGnf1h.qName) hgFixed.gnfHumanAtlas2All.name (via affyGnf1h.qName) hgFixed.gnfHumanAtlas2AllRatio.name (via affyGnf1h.qName) hgFixed.gnfHumanAtlas2Median.name (via affyGnf1h.qName) hgFixed.gnfHumanAtlas2MedianRatio.name (via affyGnf1h.qName)

Sample Rows

bin	matches	misMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
792	496	1	0	0	1	713	-	gnf1h00031_at	497	0	497	chr7	158821424	27204401	27205611	2	185,312,	0,185,	27204401,27205299,
1349	546	1	1	1	0	0	-	gnf1h00032_at	548	0	548	chr4	191273063	100263921	100264468	2	315,232,	0,316,	100263921,100264236,
1459	115	0	0	0	1	1513	-	gnf1h00033_at	115	0	115	chr4	191273063	114596401	114598029	2	25,90,	0,25,	114596401,114597939,
1459	415	0	0	0	5	55506	-	gnf1h00034_s_at	415	0	415	chr4	191273063	114598056	114653977	6	112,95,76,49,38,45,	0,112,207,283,332,370,	114598056,114600751,114606133,114641067,114650242,114653932,
883	488	0	0	0	2	17345	+	gnf1h00035_at	488	0	488	chr6	170899992	39088365	39106198	3	26,122,340,	0,26,148,	39088365,39102299,39105858,
663	535	1	0	0	3	15652	+	gnf1h00036_at	536	0	536	chr3	199501827	10239486	10255674	4	29,63,201,243,	0,29,92,293,	10239486,10243054,10251142,10255431,
966	525	2	0	0	3	12458	-	gnf1h00037_at	528	1	528	chr12	132349534	50009766	50022751	4	118,146,137,126,	0,118,264,401,	50009766,50019910,50021294,50022625,
715	563	0	0	0	5	3913	-	gnf1h00038_at	563	0	563	chr11	134452384	17067919	17072395	6	124,126,110,73,118,12,	0,124,250,360,433,551,	17067919,17069456,17069669,17070118,17070281,17072383,
1175	325	0	0	0	0	0	+	gnf1h00039_at	325	0	325	chr11	134452384	77452576	77452901	1	325,	0,	77452576,
1349	490	1	0	0	5	3261	+	gnf1h00040_at	491	0	491	chr7	158821424	100229537	100233289	6	39,139,141,100,47,25,	0,39,178,319,419,466,	100229537,100229677,100230753,100232923,100233134,100233264,

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

Affy GNF1H (affyGnf1h) Track Description


	Description This track shows the location of the sequences used for the selection of probes on the Affymetrix GNF1H chips. This contains 11406 predicted genes that do not overlap with the Affy U133A chip. Methods The sequences were mapped to the genome using blat followed by pslReps with the parameters: `-minCover=0.3 -minAli=0.95 -nearTop=0.005` Credits Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track. References Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923

Description

Methods

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