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: DobsGB1 Primary Table: RNAmmer Row Count: 37 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	587	`smallint(5) unsigned`	range
`chrom`	BDQP01000008	`varchar(255)`	values
`chromStart`	324675	`int(10) unsigned`	range
`chromEnd`	330575	`int(10) unsigned`	range
`name`	RNAmmer_28s_rRNA_1	`varchar(255)`	values
`score`	284	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	284.4	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
587	BDQP01000008	324675	330575	RNAmmer_28s_rRNA_1	284	-	284.4
587	BDQP01000008	327619	327733	RNAmmer_8s_rRNA_2	68	-	68
587	BDQP01000008	331352	332831	RNAmmer_18s_rRNA_3	219	-	219.1
591	BDQP01000008	897426	902380	RNAmmer_28s_rRNA_4	272	-	272.9
591	BDQP01000008	899424	899538	RNAmmer_8s_rRNA_5	68	-	68
591	BDQP01000008	903157	904636	RNAmmer_18s_rRNA_6	219	-	219.1
596	BDQP01000008	1467854	1467968	RNAmmer_8s_rRNA_7	68	+	68
586	BDQP01000015	149248	155559	RNAmmer_28s_rRNA_8	274	-	274.5
586	BDQP01000015	152603	152717	RNAmmer_8s_rRNA_9	68	-	68
586	BDQP01000015	156336	157815	RNAmmer_18s_rRNA_10	219	-	219.1

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.