Schema for rRNA Genes - Ribosomal RNA Genes Identified by RNAmmer

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Schema for rRNA Genes - Ribosomal RNA Genes Identified by RNAmmer

Database: DbiaGB2 Primary Table: RNAmmer Row Count: 42 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFD02001608	`varchar(255)`	values
`chromStart`	308	`int(10) unsigned`	range
`chromEnd`	1578	`int(10) unsigned`	range
`name`	RNAmmer_18s_rRNA_1	`varchar(255)`	values
`score`	414	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	414.6	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	AFFD02001608	308	1578	RNAmmer_18s_rRNA_1	414	-	414.6
585	AFFD02001609	0	1383	RNAmmer_18s_rRNA_2	414	-	414.6
585	AFFD02001660	77	1255	RNAmmer_18s_rRNA_3	488	+	488
585	AFFD02001661	0	851	RNAmmer_18s_rRNA_4	488	+	488
585	AFFD02001784	456	1495	RNAmmer_18s_rRNA_5	639	-	639.1
585	AFFD02001785	0	1091	RNAmmer_18s_rRNA_6	639	-	639.1
585	AFFD02001786	0	1759	RNAmmer_18s_rRNA_7	639	-	639.1
585	AFFD02001787	0	214	RNAmmer_18s_rRNA_8	639	-	639.1
585	AFFD02001840	2360	3877	RNAmmer_18s_rRNA_9	199	-	199.9
585	AFFD02002033	63	1684	RNAmmer_18s_rRNA_10	385	+	385.5

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

rRNA Genes (RNAmmer) Track Description


	Description This track shows the rRNA gene predictions produced by RNAmmer using the parameters: `-S euk -m lsu,ssu,tsu`. References Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-8.