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: DgriCAF1 Primary Table: RNAmmer Row Count: 55 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_12429	`varchar(255)`	values
`chromStart`	70	`int(10) unsigned`	range
`chromEnd`	185	`int(10) unsigned`	range
`name`	RNAmmer_8s_rRNA_1	`varchar(255)`	values
`score`	75	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	75.5	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	scaffold_12429	70	185	RNAmmer_8s_rRNA_1	75	-	75.5
585	scaffold_14977	3990	4105	RNAmmer_8s_rRNA_2	75	-	75.5
585	scaffold_14977	37374	37489	RNAmmer_8s_rRNA_3	75	-	75.5
585	scaffold_14977	40617	40732	RNAmmer_8s_rRNA_4	75	-	75.5
585	scaffold_14977	44315	44430	RNAmmer_8s_rRNA_5	75	-	75.5
585	scaffold_14977	47555	47670	RNAmmer_8s_rRNA_6	75	-	75.5
585	scaffold_14977	51386	51501	RNAmmer_8s_rRNA_7	75	-	75.5
585	scaffold_14977	53658	53773	RNAmmer_8s_rRNA_8	75	-	75.5
588	scaffold_14978	484429	484544	RNAmmer_8s_rRNA_9	75	+	75.5
588	scaffold_14978	489632	489747	RNAmmer_8s_rRNA_10	75	+	75.5

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.