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: DbipGB2 Primary Table: RNAmmer Row Count: 19 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFE02004649	`varchar(255)`	values
`chromStart`	5090	`int(10) unsigned`	range
`chromEnd`	6378	`int(10) unsigned`	range
`name`	RNAmmer_28s_rRNA_1	`varchar(255)`	values
`score`	81	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	81.1	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	AFFE02004649	5090	6378	RNAmmer_28s_rRNA_1	81	-	81.1
585	AFFE02004652	304	418	RNAmmer_8s_rRNA_2	46	+	46.9
585	AFFE02004713	781	1351	RNAmmer_28s_rRNA_3	132	+	132.5
585	AFFE02004714	0	1380	RNAmmer_28s_rRNA_4	132	+	132.5
585	AFFE02004715	0	1119	RNAmmer_28s_rRNA_5	132	+	132.5
585	AFFE02004716	0	1238	RNAmmer_28s_rRNA_6	132	+	132.5
585	AFFE02004717	0	1353	RNAmmer_28s_rRNA_7	132	+	132.5
585	AFFE02007569	1102	1219	RNAmmer_8s_rRNA_8	50	-	50.2
585	KB463212	34972	35086	RNAmmer_8s_rRNA_9	66	-	66.2
585	KB463219	55387	55501	RNAmmer_8s_rRNA_10	66	-	66.2

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.