Schema for RNA-seq Breast - Burge Lab RNA-seq 32mer Reads from Breast

Database: hg19 Primary Table: burgeRnaSeqGemMapperAlignBreast Row Count: 10,557,297
Format description: Browser extensible data

field	example	SQL type	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	Reference sequence chromosome or scaffold
`chromStart`	14924	`int(10) unsigned`	Start position in chromosome
`chromEnd`	14956	`int(10) unsigned`	End position in chromosome
`name`	GSM325486_HCT202_s2468__116...	`varchar(255)`	Name of item
`score`	1000	`int(10) unsigned`	Score from 0-1000
`strand`	-	`char(1)`	+ or -
`thickStart`	0	`int(10) unsigned`	Start of where display should be thick (start codon)
`thickEnd`	0	`int(10) unsigned`	End of where display should be thick (stop codon)
`reserved`	0	`int(10) unsigned`	Used as itemRgb as of 2004-11-22
`blockCount`	1	`int(10) unsigned`	Number of blocks
`blockSizes`	32,	`longblob`	Comma separated list of block sizes
`chromStarts`	0,	`longblob`	Start positions relative to chromStart

bin	chrom	chromStart	chromEnd	name	score	strand	blockCount	blockSizes	chromStarts
585	chr1	14924	14956	GSM325486_HCT202_s2468__11652820_chr1_14925_14956	1000	-	1	32,	0,
585	chr1	16789	16821	GSM325486_HCT202_s2468__1825333_chr1_16790_16821	1000	-	1	32,	0,
585	chr1	17461	17493	GSM325486_HCT202_s2468__509131_chr1_17462_17493	1000	+	1	32,	0,
585	chr1	17461	17493	GSM325486_HCT202_s2468__9459260_chr1_17462_17493	1000	-	1	32,	0,
585	chr1	17475	17507	GSM325486_HCT202_s2468__7915409_chr1_17476_17507	1000	+	1	32,	0,
585	chr1	17476	17508	GSM325486_HCT202_s2468__7254885_chr1_17477_17508	1000	+	1	32,	0,
585	chr1	17476	17508	GSM325486_HCT202_s2468__7898997_chr1_17477_17508	1000	+	1	32,	0,
585	chr1	17490	17522	GSM325486_HCT202_s2468__14886086_chr1_17491_17522	1000	+	1	32,	0,
585	chr1	128621	128653	GSM325486_HCT202_s2468__14801485_chr1_128622_128653	1000	+	1	32,	0,
586	chr1	136033	136065	GSM325486_HCT202_s2468__14608536_chr1_136034_136065	1000	+	1	32,	0,

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