Strain Fitness in Pseudomonas simiae WCS417 around PS417_25005

Experiment: rhizosphere sample 2; outgrowth in LB

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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.

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500 ntPS417_24995 and PS417_25000 overlap by 8 nucleotidesPS417_25000 and PS417_25005 are separated by 21 nucleotidesPS417_25005 and PS417_25010 overlap by 4 nucleotides PS417_24995: PS417_24995 - exotoxin, at 5,420,615 to 5,421,130 _24995 PS417_25000: PS417_25000 - fimbrial protein, at 5,421,123 to 5,421,701 _25000 PS417_25005: PS417_25005 - molecular chaperone, at 5,421,723 to 5,422,484 _25005 PS417_25010: PS417_25010 - fimbrial assembly protein, at 5,422,481 to 5,425,000 _25010 Position (kb) 5421 5422 5423Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 5420.808 kb on + strand, within PS417_24995at 5420.866 kb on + strand, within PS417_24995at 5420.866 kb on + strand, within PS417_24995at 5420.867 kb on - strand, within PS417_24995at 5420.867 kb on - strand, within PS417_24995at 5421.004 kb on + strand, within PS417_24995at 5421.007 kb on + strand, within PS417_24995at 5421.008 kb on - strand, within PS417_24995at 5421.008 kb on - strand, within PS417_24995at 5421.086 kb on - strandat 5421.130 kb on + strandat 5421.130 kb on + strandat 5421.130 kb on + strandat 5421.131 kb on - strandat 5421.131 kb on - strandat 5421.131 kb on - strandat 5421.148 kb on - strandat 5421.150 kb on + strandat 5421.205 kb on + strand, within PS417_25000at 5421.205 kb on + strand, within PS417_25000at 5421.205 kb on + strand, within PS417_25000at 5421.205 kb on + strand, within PS417_25000at 5421.206 kb on - strand, within PS417_25000at 5421.206 kb on - strand, within PS417_25000at 5421.206 kb on - strand, within PS417_25000at 5421.206 kb on - strand, within PS417_25000at 5421.206 kb on - strand, within PS417_25000at 5421.240 kb on + strand, within PS417_25000at 5421.282 kb on + strand, within PS417_25000at 5421.282 kb on + strand, within PS417_25000at 5421.388 kb on + strand, within PS417_25000at 5421.522 kb on + strand, within PS417_25000at 5421.528 kb on + strand, within PS417_25000at 5421.596 kb on + strand, within PS417_25000at 5421.663 kb on + strandat 5421.664 kb on - strandat 5421.667 kb on - strandat 5421.667 kb on - strandat 5421.667 kb on - strandat 5421.675 kb on + strandat 5421.724 kb on + strandat 5421.764 kb on + strandat 5421.817 kb on + strand, within PS417_25005at 5421.817 kb on + strand, within PS417_25005at 5421.818 kb on - strand, within PS417_25005at 5421.818 kb on - strand, within PS417_25005at 5421.826 kb on + strand, within PS417_25005at 5421.826 kb on + strand, within PS417_25005at 5421.827 kb on - strand, within PS417_25005at 5421.867 kb on + strand, within PS417_25005at 5421.867 kb on + strand, within PS417_25005at 5421.868 kb on - strand, within PS417_25005at 5421.868 kb on - strand, within PS417_25005at 5421.868 kb on - strand, within PS417_25005at 5421.868 kb on - strand, within PS417_25005at 5421.878 kb on + strandat 5421.885 kb on + strand, within PS417_25005at 5421.886 kb on - strand, within PS417_25005at 5421.927 kb on - strand, within PS417_25005at 5421.955 kb on + strand, within PS417_25005at 5421.956 kb on - strand, within PS417_25005at 5421.956 kb on - strand, within PS417_25005at 5421.956 kb on - strand, within PS417_25005at 5421.958 kb on + strand, within PS417_25005at 5421.959 kb on - strand, within PS417_25005at 5421.971 kb on + strand, within PS417_25005at 5422.056 kb on - strand, within PS417_25005at 5422.056 kb on - strand, within PS417_25005at 5422.314 kb on + strand, within PS417_25005at 5422.314 kb on + strand, within PS417_25005at 5422.324 kb on - strand, within PS417_25005at 5422.335 kb on - strand, within PS417_25005at 5422.651 kb on + strandat 5422.735 kb on + strand, within PS417_25010at 5422.787 kb on + strand, within PS417_25010at 5422.788 kb on - strand, within PS417_25010at 5422.788 kb on - strand, within PS417_25010at 5422.857 kb on - strand, within PS417_25010at 5422.857 kb on - strand, within PS417_25010at 5422.933 kb on - strand, within PS417_25010at 5422.948 kb on - strandat 5422.972 kb on + strand, within PS417_25010at 5422.973 kb on - strand, within PS417_25010at 5423.000 kb on + strand, within PS417_25010at 5423.000 kb on + strand, within PS417_25010at 5423.000 kb on + strand, within PS417_25010at 5423.027 kb on - strand, within PS417_25010at 5423.095 kb on + strand, within PS417_25010at 5423.096 kb on - strand, within PS417_25010at 5423.125 kb on + strand, within PS417_25010at 5423.125 kb on + strand, within PS417_25010at 5423.125 kb on + strand, within PS417_25010at 5423.126 kb on - strand, within PS417_25010at 5423.126 kb on - strand, within PS417_25010at 5423.147 kb on - strand, within PS417_25010at 5423.183 kb on - strand, within PS417_25010at 5423.230 kb on - strand, within PS417_25010at 5423.230 kb on - strandat 5423.230 kb on - strand, within PS417_25010at 5423.236 kb on + strand, within PS417_25010at 5423.236 kb on + strand, within PS417_25010at 5423.236 kb on + strand, within PS417_25010at 5423.237 kb on - strand, within PS417_25010at 5423.353 kb on + strand, within PS417_25010at 5423.354 kb on - strand, within PS417_25010at 5423.360 kb on - strand, within PS417_25010at 5423.372 kb on - strand, within PS417_25010at 5423.437 kb on - strand, within PS417_25010at 5423.484 kb on + strand, within PS417_25010

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Per-strain Table

Position Strand Gene LocusTag Fraction rhizosphere sample 2; outgrowth in LB
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5,420,808 + PS417_24995 0.37 +2.2
5,420,866 + PS417_24995 0.49 -1.8
5,420,866 + PS417_24995 0.49 -1.5
5,420,867 - PS417_24995 0.49 +0.2
5,420,867 - PS417_24995 0.49 -0.5
5,421,004 + PS417_24995 0.75 +2.4
5,421,007 + PS417_24995 0.76 -0.1
5,421,008 - PS417_24995 0.76 +0.3
5,421,008 - PS417_24995 0.76 +0.7
5,421,086 - +0.5
5,421,130 + +0.3
5,421,130 + -0.6
5,421,130 + +2.6
5,421,131 - +1.0
5,421,131 - -0.6
5,421,131 - +0.2
5,421,148 - +0.1
5,421,150 + -0.4
5,421,205 + PS417_25000 0.14 -0.3
5,421,205 + PS417_25000 0.14 +0.5
5,421,205 + PS417_25000 0.14 +2.1
5,421,205 + PS417_25000 0.14 -0.5
5,421,206 - PS417_25000 0.14 -2.6
5,421,206 - PS417_25000 0.14 -0.3
5,421,206 - PS417_25000 0.14 +1.0
5,421,206 - PS417_25000 0.14 +1.4
5,421,206 - PS417_25000 0.14 -0.2
5,421,240 + PS417_25000 0.20 +1.2
5,421,282 + PS417_25000 0.27 -0.8
5,421,282 + PS417_25000 0.27 +1.8
5,421,388 + PS417_25000 0.46 +0.9
5,421,522 + PS417_25000 0.69 -0.5
5,421,528 + PS417_25000 0.70 +0.1
5,421,596 + PS417_25000 0.82 -1.6
5,421,663 + -0.6
5,421,664 - +0.1
5,421,667 - +0.3
5,421,667 - -0.5
5,421,667 - +0.2
5,421,675 + +0.2
5,421,724 + +0.3
5,421,764 + -0.2
5,421,817 + PS417_25005 0.12 -1.2
5,421,817 + PS417_25005 0.12 +0.0
5,421,818 - PS417_25005 0.12 -0.7
5,421,818 - PS417_25005 0.12 -1.0
5,421,826 + PS417_25005 0.14 -0.6
5,421,826 + PS417_25005 0.14 +0.4
5,421,827 - PS417_25005 0.14 -1.7
5,421,867 + PS417_25005 0.19 -0.5
5,421,867 + PS417_25005 0.19 -1.2
5,421,868 - PS417_25005 0.19 +2.1
5,421,868 - PS417_25005 0.19 -2.8
5,421,868 - PS417_25005 0.19 -0.2
5,421,868 - PS417_25005 0.19 -0.4
5,421,878 + +1.5
5,421,885 + PS417_25005 0.21 -1.9
5,421,886 - PS417_25005 0.21 -0.2
5,421,927 - PS417_25005 0.27 -0.5
5,421,955 + PS417_25005 0.30 -0.6
5,421,956 - PS417_25005 0.31 +1.5
5,421,956 - PS417_25005 0.31 -0.7
5,421,956 - PS417_25005 0.31 +0.4
5,421,958 + PS417_25005 0.31 +0.9
5,421,959 - PS417_25005 0.31 -0.1
5,421,971 + PS417_25005 0.33 -1.6
5,422,056 - PS417_25005 0.44 -0.1
5,422,056 - PS417_25005 0.44 -2.5
5,422,314 + PS417_25005 0.78 +0.7
5,422,314 + PS417_25005 0.78 -0.7
5,422,324 - PS417_25005 0.79 -1.5
5,422,335 - PS417_25005 0.80 -1.4
5,422,651 + +0.4
5,422,735 + PS417_25010 0.10 -2.7
5,422,787 + PS417_25010 0.12 -0.4
5,422,788 - PS417_25010 0.12 +0.8
5,422,788 - PS417_25010 0.12 -0.3
5,422,857 - PS417_25010 0.15 +0.0
5,422,857 - PS417_25010 0.15 +0.8
5,422,933 - PS417_25010 0.18 -1.1
5,422,948 - +1.1
5,422,972 + PS417_25010 0.19 +1.8
5,422,973 - PS417_25010 0.20 +1.1
5,423,000 + PS417_25010 0.21 +0.2
5,423,000 + PS417_25010 0.21 -0.1
5,423,000 + PS417_25010 0.21 -1.0
5,423,027 - PS417_25010 0.22 -0.4
5,423,095 + PS417_25010 0.24 -1.8
5,423,096 - PS417_25010 0.24 +0.7
5,423,125 + PS417_25010 0.26 +1.2
5,423,125 + PS417_25010 0.26 -0.5
5,423,125 + PS417_25010 0.26 -0.4
5,423,126 - PS417_25010 0.26 -0.3
5,423,126 - PS417_25010 0.26 +0.2
5,423,147 - PS417_25010 0.26 -0.4
5,423,183 - PS417_25010 0.28 -0.2
5,423,230 - PS417_25010 0.30 -0.3
5,423,230 - +3.1
5,423,230 - PS417_25010 0.30 +0.5
5,423,236 + PS417_25010 0.30 +0.1
5,423,236 + PS417_25010 0.30 +0.1
5,423,236 + PS417_25010 0.30 +1.1
5,423,237 - PS417_25010 0.30 -1.2
5,423,353 + PS417_25010 0.35 -1.6
5,423,354 - PS417_25010 0.35 +0.8
5,423,360 - PS417_25010 0.35 -0.1
5,423,372 - PS417_25010 0.35 -0.9
5,423,437 - PS417_25010 0.38 +0.2
5,423,484 + PS417_25010 0.40 +0.3

Or see this region's nucleotide sequence