Strain Fitness in Variovorax sp. SCN45 around GFF4301

Experiment: Community=arabino-guar; Passage=4

Add experiment(s):

Zoom: Pan:

Only strains with sufficient reads to estimate fitness are shown, but the strain fitness values are still rather noisy and may be biased towards zero. Strains near the edge of a gene are not shown as being associated with that gene (they are in grey). Strains in the central 10-90% of a gene are color coded by the insertion's strand. Usually, "+" means that the selectable marker is encoded on the forward strand, i.e., transcribed rightward.

download SVG
500 ntGFF4300 and GFF4301 are separated by 139 nucleotidesGFF4301 and GFF4302 are separated by 42 nucleotides GFF4300 - Hydroxymethylglutaryl-CoA synthase (EC 2.3.3.10) / conserved protein associated with acetyl-CoA C-acyltransferase, at 219,210 to 220,691 GFF4300 GFF4301 - Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases), at 220,831 to 221,745 GFF4301 GFF4302 - hypothetical protein AF1210, at 221,788 to 222,720 GFF4302 Position (kb) 220 221 222Strain fitness (log2 ratio) -3 -2 -1 0 1at 220.069 kb on + strand, within GFF4300at 220.612 kb on - strandat 220.695 kb on + strandat 220.722 kb on + strandat 221.270 kb on - strand, within GFF4301at 221.594 kb on - strand, within GFF4301at 222.059 kb on - strand, within GFF4302at 222.238 kb on + strand, within GFF4302at 222.305 kb on - strand, within GFF4302at 222.322 kb on + strand, within GFF4302at 222.322 kb on + strand, within GFF4302

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction Community=arabino-guar; Passage=4
remove
220,069 + GFF4300 0.58 -3.4
220,612 - -1.3
220,695 + +0.7
220,722 + -2.4
221,270 - GFF4301 0.48 +1.1
221,594 - GFF4301 0.83 +0.8
222,059 - GFF4302 0.29 -0.9
222,238 + GFF4302 0.48 -0.3
222,305 - GFF4302 0.55 -0.9
222,322 + GFF4302 0.57 -2.7
222,322 + GFF4302 0.57 +0.7

Or see this region's nucleotide sequence