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: DvirCAF1 Primary Table: RNAmmer Row Count: 83 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_11162	`varchar(255)`	values
`chromStart`	103	`int(10) unsigned`	range
`chromEnd`	1134	`int(10) unsigned`	range
`name`	RNAmmer_18s_rRNA_1	`varchar(255)`	values
`score`	134	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	134.3	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	scaffold_11162	103	1134	RNAmmer_18s_rRNA_1	134	-	134.3
585	scaffold_11163	0	804	RNAmmer_18s_rRNA_2	134	-	134.3
585	scaffold_12720	38450	40444	RNAmmer_18s_rRNA_3	1000	-	1280.1
615	scaffold_12875	4016163	4016278	RNAmmer_8s_rRNA_4	76	+	76.9
615	scaffold_12875	4016671	4016786	RNAmmer_8s_rRNA_5	76	+	76.9
615	scaffold_12875	4017180	4017295	RNAmmer_8s_rRNA_6	76	+	76.9
621	scaffold_12875	4760252	4760367	RNAmmer_8s_rRNA_7	76	+	76.9
621	scaffold_12875	4764789	4764904	RNAmmer_8s_rRNA_8	76	-	76.9
621	scaffold_12875	4775526	4775641	RNAmmer_8s_rRNA_9	76	-	76.9
621	scaffold_12875	4793933	4794048	RNAmmer_8s_rRNA_10	76	+	76.9

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.