Strain Fitness in Variovorax sp. SCN45 around GFF4

Experiment: Community=Locust bean gum; 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 ntGFF2 and GFF3 are separated by 63 nucleotidesGFF3 and GFF4 are separated by 7 nucleotidesGFF4 and GFF5 overlap by 4 nucleotides GFF2 - Transcription accessory protein (S1 RNA-binding domain), at 1,164 to 3,539 GFF2 GFF3 - VapB protein (antitoxin to VapC), at 3,603 to 3,860 GFF3 GFF4 - VapC toxin protein, at 3,868 to 4,281 GFF4 GFF5 - FIG00537881: hypothetical protein, at 4,278 to 5,351 GFF5 Position (kb) 3 4 5Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3 4at 2.940 kb on + strand, within GFF2at 2.940 kb on + strand, within GFF2at 2.940 kb on + strand, within GFF2at 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.537 kb on + strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.538 kb on - strandat 3.541 kb on + strandat 3.541 kb on + strandat 3.541 kb on + strandat 3.541 kb on + strandat 3.542 kb on - strandat 3.542 kb on - strandat 3.542 kb on - strandat 3.542 kb on - strandat 3.571 kb on + strandat 3.572 kb on - strandat 3.871 kb on + strandat 3.871 kb on + strandat 3.871 kb on + strandat 3.871 kb on + strandat 3.871 kb on + strandat 3.872 kb on - strandat 3.872 kb on - strandat 3.872 kb on - strandat 3.872 kb on - strandat 3.872 kb on - strandat 3.872 kb on - strandat 4.081 kb on + strand, within GFF4at 4.081 kb on + strand, within GFF4at 4.081 kb on + strand, within GFF4at 4.081 kb on + strand, within GFF4at 4.081 kb on + strand, within GFF4at 4.081 kb on + strand, within GFF4at 4.082 kb on - strand, within GFF4at 4.082 kb on - strand, within GFF4at 4.082 kb on - strand, within GFF4at 4.082 kb on - strand, within GFF4at 4.082 kb on - strand, within GFF4at 4.156 kb on + strand, within GFF4at 4.156 kb on + strand, within GFF4at 4.157 kb on - strand, within GFF4at 4.157 kb on - strand, within GFF4at 4.157 kb on - strand, within GFF4at 4.157 kb on - strand, within GFF4at 4.157 kb on - strand, within GFF4at 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.250 kb on + strandat 4.251 kb on - strandat 4.251 kb on - strandat 4.251 kb on - strandat 4.251 kb on - strandat 4.251 kb on - strandat 4.251 kb on - strandat 4.296 kb on + strandat 4.296 kb on + strandat 4.296 kb on + strandat 4.296 kb on + strandat 4.297 kb on - strandat 4.297 kb on - strandat 4.297 kb on - strandat 4.297 kb on - strandat 4.548 kb on + strand, within GFF5at 4.548 kb on + strand, within GFF5at 4.549 kb on - strand, within GFF5at 4.549 kb on - strand, within GFF5at 4.641 kb on + strand, within GFF5at 4.755 kb on + strand, within GFF5at 4.755 kb on + strand, within GFF5at 4.755 kb on + strand, within GFF5at 4.756 kb on - strand, within GFF5at 4.756 kb on - strand, within GFF5at 4.756 kb on - strand, within GFF5at 4.986 kb on + strand, within GFF5at 5.010 kb on + strand, within GFF5at 5.010 kb on + strand, within GFF5at 5.011 kb on - strand, within GFF5at 5.011 kb on - strand, within GFF5at 5.028 kb on + strand, within GFF5at 5.058 kb on + strand, within GFF5

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction Community=Locust bean gum; Passage=4
remove
2,940 + GFF2 0.75 -1.6
2,940 + GFF2 0.75 -1.1
2,940 + GFF2 0.75 -3.4
3,537 + -0.2
3,537 + +0.4
3,537 + +1.8
3,537 + +0.7
3,537 + +1.3
3,537 + +0.6
3,537 + -1.1
3,537 + -1.1
3,537 + -2.2
3,537 + -1.1
3,538 - -1.7
3,538 - -0.2
3,538 - -3.7
3,538 - -0.8
3,538 - +1.6
3,538 - -1.9
3,538 - -1.8
3,538 - +1.4
3,538 - -0.6
3,538 - +0.1
3,538 - +0.2
3,538 - -1.1
3,541 + +0.7
3,541 + -3.0
3,541 + +0.4
3,541 + +0.5
3,542 - -1.8
3,542 - +2.8
3,542 - +0.8
3,542 - +0.5
3,571 + -0.1
3,572 - -2.1
3,871 + +0.0
3,871 + +3.8
3,871 + -1.0
3,871 + -0.3
3,871 + +0.1
3,872 - -0.7
3,872 - -0.7
3,872 - -0.9
3,872 - -0.2
3,872 - +0.2
3,872 - -0.8
4,081 + GFF4 0.51 -2.0
4,081 + GFF4 0.51 +0.1
4,081 + GFF4 0.51 -1.1
4,081 + GFF4 0.51 -1.1
4,081 + GFF4 0.51 -2.7
4,081 + GFF4 0.51 +0.5
4,082 - GFF4 0.52 +0.4
4,082 - GFF4 0.52 +0.5
4,082 - GFF4 0.52 -1.0
4,082 - GFF4 0.52 -0.6
4,082 - GFF4 0.52 +1.8
4,156 + GFF4 0.70 -3.0
4,156 + GFF4 0.70 -0.8
4,157 - GFF4 0.70 -4.0
4,157 - GFF4 0.70 -2.0
4,157 - GFF4 0.70 -1.2
4,157 - GFF4 0.70 -2.1
4,157 - GFF4 0.70 -0.5
4,250 + +1.2
4,250 + +0.3
4,250 + -2.1
4,250 + -3.6
4,250 + -0.2
4,250 + -1.5
4,250 + -1.3
4,250 + -1.4
4,250 + -1.5
4,250 + -2.1
4,251 - -1.1
4,251 - -1.2
4,251 - +1.2
4,251 - -0.2
4,251 - -0.0
4,251 - -1.3
4,296 + +0.1
4,296 + +1.8
4,296 + -0.1
4,296 + +0.8
4,297 - +1.5
4,297 - -2.2
4,297 - -0.4
4,297 - +1.9
4,548 + GFF5 0.25 +1.8
4,548 + GFF5 0.25 +0.5
4,549 - GFF5 0.25 -1.3
4,549 - GFF5 0.25 +2.5
4,641 + GFF5 0.34 +0.4
4,755 + GFF5 0.44 -2.6
4,755 + GFF5 0.44 -2.2
4,755 + GFF5 0.44 +0.2
4,756 - GFF5 0.45 -1.6
4,756 - GFF5 0.45 -0.7
4,756 - GFF5 0.45 +1.4
4,986 + GFF5 0.66 -2.2
5,010 + GFF5 0.68 +0.5
5,010 + GFF5 0.68 +0.5
5,011 - GFF5 0.68 -1.1
5,011 - GFF5 0.68 +0.2
5,028 + GFF5 0.70 -0.2
5,058 + GFF5 0.73 -0.8

Or see this region's nucleotide sequence