Strain Fitness in Variovorax sp. SCN45 around GFF3015

Experiment: M9 with calcium pantothenate 10 mg/mL

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 ntGFF3013 and GFF3014 are separated by 29 nucleotidesGFF3014 and GFF3015 are separated by 1 nucleotidesGFF3015 and GFF3016 overlap by 4 nucleotides GFF3013 - KEGG: type VI secretion system secreted protein Hcp, at 440,289 to 440,771 GFF3013 GFF3014 - KEGG: type VI secretion system protein ImpF, at 440,801 to 441,259 GFF3014 GFF3015 - T6SS component TssF (ImpG/VasA), at 441,261 to 443,072 GFF3015 GFF3016 - T6SS component TssG (ImpH/VasB), at 443,069 to 444,082 GFF3016 Position (kb) 441 442 443 444Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.294 kb on + strandat 440.295 kb on - strandat 440.295 kb on - strandat 440.295 kb on - strandat 440.295 kb on - strandat 440.295 kb on - strandat 440.298 kb on + strandat 440.298 kb on + strandat 440.299 kb on - strandat 440.299 kb on - strandat 440.299 kb on - strandat 440.667 kb on + strand, within GFF3013at 440.667 kb on + strand, within GFF3013at 440.667 kb on + strand, within GFF3013at 440.668 kb on - strand, within GFF3013at 440.668 kb on - strand, within GFF3013at 440.668 kb on - strand, within GFF3013at 440.688 kb on + strand, within GFF3013at 440.688 kb on + strand, within GFF3013at 440.689 kb on - strand, within GFF3013at 440.689 kb on - strand, within GFF3013at 440.972 kb on + strand, within GFF3014at 441.002 kb on + strand, within GFF3014at 441.002 kb on + strand, within GFF3014at 441.003 kb on - strand, within GFF3014at 441.093 kb on - strand, within GFF3014at 441.294 kb on + strandat 441.294 kb on + strandat 441.295 kb on - strandat 441.295 kb on - strandat 441.295 kb on - strandat 441.297 kb on + strandat 441.297 kb on + strandat 441.298 kb on - strandat 441.298 kb on - strandat 441.315 kb on + strandat 441.408 kb on - strandat 441.755 kb on - strand, within GFF3015at 441.755 kb on - strand, within GFF3015at 441.861 kb on + strand, within GFF3015at 441.861 kb on + strand, within GFF3015at 441.861 kb on + strand, within GFF3015at 441.862 kb on - strand, within GFF3015at 442.008 kb on + strand, within GFF3015at 442.008 kb on + strand, within GFF3015at 442.026 kb on + strand, within GFF3015at 442.027 kb on - strand, within GFF3015at 442.240 kb on - strand, within GFF3015at 442.240 kb on - strand, within GFF3015at 442.245 kb on + strand, within GFF3015at 442.245 kb on + strand, within GFF3015at 442.246 kb on - strand, within GFF3015at 442.246 kb on - strand, within GFF3015at 442.246 kb on - strand, within GFF3015at 442.246 kb on - strand, within GFF3015at 442.246 kb on - strand, within GFF3015at 442.527 kb on + strand, within GFF3015at 442.527 kb on + strand, within GFF3015at 442.527 kb on + strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.528 kb on - strand, within GFF3015at 442.632 kb on + strand, within GFF3015at 442.873 kb on - strand, within GFF3015at 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.974 kb on + strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strandat 442.975 kb on - strand

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction M9 with calcium pantothenate 10 mg/mL
remove
440,294 + -0.0
440,294 + -0.9
440,294 + +1.3
440,294 + -1.4
440,294 + -1.7
440,294 + +0.2
440,294 + +0.6
440,294 + +0.2
440,294 + -0.4
440,294 + -0.1
440,295 - -1.1
440,295 - +1.0
440,295 - +0.4
440,295 - -0.1
440,295 - +0.1
440,298 + +0.0
440,298 + +1.8
440,299 - -0.3
440,299 - +0.6
440,299 - -0.1
440,667 + GFF3013 0.78 +0.4
440,667 + GFF3013 0.78 +1.0
440,667 + GFF3013 0.78 +0.6
440,668 - GFF3013 0.78 +1.2
440,668 - GFF3013 0.78 +0.2
440,668 - GFF3013 0.78 +0.2
440,688 + GFF3013 0.83 +0.8
440,688 + GFF3013 0.83 +0.6
440,689 - GFF3013 0.83 -1.6
440,689 - GFF3013 0.83 -0.6
440,972 + GFF3014 0.37 -1.1
441,002 + GFF3014 0.44 -1.4
441,002 + GFF3014 0.44 +0.4
441,003 - GFF3014 0.44 -1.2
441,093 - GFF3014 0.64 -1.3
441,294 + +0.1
441,294 + +1.4
441,295 - -1.1
441,295 - +0.6
441,295 - -0.3
441,297 + -1.6
441,297 + +0.0
441,298 - -0.7
441,298 - -0.5
441,315 + -0.2
441,408 - -0.7
441,755 - GFF3015 0.27 -0.7
441,755 - GFF3015 0.27 +0.5
441,861 + GFF3015 0.33 -0.9
441,861 + GFF3015 0.33 -0.2
441,861 + GFF3015 0.33 -1.1
441,862 - GFF3015 0.33 -2.2
442,008 + GFF3015 0.41 -1.8
442,008 + GFF3015 0.41 -0.2
442,026 + GFF3015 0.42 -0.5
442,027 - GFF3015 0.42 -1.1
442,240 - GFF3015 0.54 -0.1
442,240 - GFF3015 0.54 -0.4
442,245 + GFF3015 0.54 +0.2
442,245 + GFF3015 0.54 -0.4
442,246 - GFF3015 0.54 -0.1
442,246 - GFF3015 0.54 +0.2
442,246 - GFF3015 0.54 -0.7
442,246 - GFF3015 0.54 +2.2
442,246 - GFF3015 0.54 -2.8
442,527 + GFF3015 0.70 -1.0
442,527 + GFF3015 0.70 -0.2
442,527 + GFF3015 0.70 +0.2
442,528 - GFF3015 0.70 +0.2
442,528 - GFF3015 0.70 -1.4
442,528 - GFF3015 0.70 +0.4
442,528 - GFF3015 0.70 -0.2
442,528 - GFF3015 0.70 +0.1
442,528 - GFF3015 0.70 -0.8
442,632 + GFF3015 0.76 -0.6
442,873 - GFF3015 0.89 +0.3
442,974 + -0.0
442,974 + -1.0
442,974 + -0.3
442,974 + +0.2
442,974 + +0.6
442,974 + -0.5
442,974 + -0.7
442,974 + -1.0
442,974 + +0.5
442,974 + -0.6
442,974 + +0.5
442,974 + -1.4
442,974 + +0.2
442,975 - +1.1
442,975 - -1.2
442,975 - -1.2
442,975 - -0.2
442,975 - +1.9
442,975 - -0.2
442,975 - +0.8
442,975 - +2.8
442,975 - -1.2

Or see this region's nucleotide sequence