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: DtakGB2 Primary Table: RNAmmer Row Count: 27 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFI02001507	`varchar(255)`	values
`chromStart`	383	`int(10) unsigned`	range
`chromEnd`	1008	`int(10) unsigned`	range
`name`	RNAmmer_18s_rRNA_1	`varchar(255)`	values
`score`	146	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`hmmScore`	146.3	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	AFFI02001507	383	1008	RNAmmer_18s_rRNA_1	146	+	146.3
585	AFFI02001508	0	1114	RNAmmer_18s_rRNA_2	146	+	146.3
585	AFFI02001509	0	338	RNAmmer_18s_rRNA_3	146	+	146.3
585	AFFI02001576	198	1331	RNAmmer_18s_rRNA_4	490	+	490.2
585	AFFI02001606	834	1491	RNAmmer_18s_rRNA_5	165	-	165.4
585	AFFI02001607	0	834	RNAmmer_18s_rRNA_6	165	-	165.4
585	AFFI02002866	0	1420	RNAmmer_28s_rRNA_7	508	-	508.8
585	AFFI02002866	0	1420	RNAmmer_28s_rRNA_8	508	-	508.8
585	AFFI02002867	0	865	RNAmmer_28s_rRNA_10	508	-	508.8
585	AFFI02002867	0	865	RNAmmer_28s_rRNA_9	508	-	508.8

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.