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: DereCAF1 Primary Table: RNAmmer Row Count: 49 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_2564	`varchar(255)`	values
`chromStart`	64	`int(10) unsigned`	range
`chromEnd`	179	`int(10) unsigned`	range
`name`	RNAmmer_8s_rRNA_1	`varchar(255)`	values
`score`	77	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	77.1	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	scaffold_2564	64	179	RNAmmer_8s_rRNA_1	77	-	77.1
585	scaffold_2564	502	617	RNAmmer_8s_rRNA_2	77	-	77
585	scaffold_2564	2585	2700	RNAmmer_8s_rRNA_3	77	-	77.8
585	scaffold_2564	3023	3137	RNAmmer_8s_rRNA_4	63	-	63.1
585	scaffold_2642	0	111	RNAmmer_8s_rRNA_5	75	-	75
585	scaffold_2642	434	548	RNAmmer_8s_rRNA_6	77	-	77.4
585	scaffold_2642	871	986	RNAmmer_8s_rRNA_7	77	-	77.8
585	scaffold_2642	1301	1416	RNAmmer_8s_rRNA_8	77	-	77.8
585	scaffold_2642	1731	1846	RNAmmer_8s_rRNA_9	77	-	77.8
585	scaffold_2642	2169	2284	RNAmmer_8s_rRNA_10	77	-	77.8

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.