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: DeugGB2 Primary Table: RNAmmer Row Count: 40 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFPQ02001250	`varchar(255)`	values
`chromStart`	7342	`int(10) unsigned`	range
`chromEnd`	7456	`int(10) unsigned`	range
`name`	RNAmmer_8s_rRNA_1	`varchar(255)`	values
`score`	72	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`hmmScore`	72.7	`float`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	hmmScore
585	AFPQ02001250	7342	7456	RNAmmer_8s_rRNA_1	72	-	72.7
585	AFPQ02001271	594	1227	RNAmmer_18s_rRNA_2	431	+	431.3
585	AFPQ02001272	0	1470	RNAmmer_18s_rRNA_3	431	+	431.3
585	AFPQ02001273	0	1057	RNAmmer_18s_rRNA_4	431	+	431.3
585	AFPQ02001274	0	1033	RNAmmer_18s_rRNA_5	431	+	431.3
585	AFPQ02001331	235	349	RNAmmer_8s_rRNA_6	68	+	68
585	AFPQ02001364	11517	11726	RNAmmer_18s_rRNA_7	745	-	745.1
585	AFPQ02001365	0	1215	RNAmmer_18s_rRNA_8	745	-	745.1
585	AFPQ02001366	0	2232	RNAmmer_18s_rRNA_9	745	-	745.1
585	AFPQ02001453	36	1177	RNAmmer_18s_rRNA_10	455	+	455.7

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.