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: DpseGB3 Primary Table: RNAmmer Row Count: 62 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH475501	`varchar(255)`	values
`chromStart`	1569	`int(10) unsigned`	range
`chromEnd`	4843	`int(10) unsigned`	range
`name`	RNAmmer_18s_rRNA_1	`varchar(255)`	values
`score`	977	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`hmmScore`	977.6	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	CH475501	1569	4843	RNAmmer_18s_rRNA_1	977	+	977.6
585	CH475557	4140	4255	RNAmmer_8s_rRNA_2	77	+	77.5
585	CH475557	4577	4692	RNAmmer_8s_rRNA_3	77	+	77.5
585	CH475568	18639	18754	RNAmmer_8s_rRNA_4	6	+	6.5
585	CH475568	19090	19205	RNAmmer_8s_rRNA_5	77	+	77.5
585	CH475601	0	1836	RNAmmer_18s_rRNA_6	1000	-	1164.1
585	CH475601	8901	14452	RNAmmer_28s_rRNA_7	199	-	199.2
585	CH475750	1495	1610	RNAmmer_8s_rRNA_8	77	-	77.5
585	CH475804	15137	15252	RNAmmer_8s_rRNA_9	72	+	72.6
585	CH475931	2419	3806	RNAmmer_18s_rRNA_10	143	-	143.4

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.