Strain Fitness in Burkholderia phytofirmans PsJN around BPHYT_RS18505

Experiment: Plant=switchgrass; PlantTreatment=high_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=LB_with_kan50; Time=3weeks; NumberPlantsPooled=10

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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 ntBPHYT_RS18500 and BPHYT_RS18505 are separated by 334 nucleotidesBPHYT_RS18505 and BPHYT_RS18510 are separated by 82 nucleotidesBPHYT_RS18510 and BPHYT_RS18515 are separated by 0 nucleotides BPHYT_RS18500: BPHYT_RS18500 - hypothetical protein, at 4,161,677 to 4,162,588 _RS18500 BPHYT_RS18505: BPHYT_RS18505 - amino acid dehydrogenase, at 4,162,923 to 4,164,149 _RS18505 BPHYT_RS18510: BPHYT_RS18510 - endoribonuclease L-PSP, at 4,164,232 to 4,164,585 _RS18510 BPHYT_RS18515: BPHYT_RS18515 - hypothetical protein, at 4,164,586 to 4,164,789 _RS18515 Position (kb) 4162 4163 4164 4165Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 4162.018 kb on + strand, within BPHYT_RS18500at 4162.100 kb on - strand, within BPHYT_RS18500at 4162.100 kb on - strand, within BPHYT_RS18500at 4162.149 kb on + strand, within BPHYT_RS18500at 4162.149 kb on + strand, within BPHYT_RS18500at 4162.149 kb on + strand, within BPHYT_RS18500at 4162.150 kb on - strand, within BPHYT_RS18500at 4162.150 kb on - strand, within BPHYT_RS18500at 4162.327 kb on - strand, within BPHYT_RS18500at 4162.359 kb on - strand, within BPHYT_RS18500at 4162.389 kb on + strand, within BPHYT_RS18500at 4162.390 kb on - strand, within BPHYT_RS18500at 4162.458 kb on - strand, within BPHYT_RS18500at 4162.458 kb on - strand, within BPHYT_RS18500at 4162.465 kb on + strand, within BPHYT_RS18500at 4162.466 kb on - strand, within BPHYT_RS18500at 4162.466 kb on - strand, within BPHYT_RS18500at 4162.534 kb on + strandat 4162.535 kb on - strandat 4162.577 kb on - strandat 4162.701 kb on + strandat 4162.771 kb on + strandat 4162.772 kb on - strandat 4162.797 kb on + strandat 4162.798 kb on - strandat 4162.866 kb on - strandat 4162.971 kb on + strandat 4162.993 kb on - strandat 4162.993 kb on - strandat 4163.005 kb on + strandat 4163.067 kb on + strand, within BPHYT_RS18505at 4163.068 kb on - strand, within BPHYT_RS18505at 4163.068 kb on - strandat 4163.073 kb on + strand, within BPHYT_RS18505at 4163.073 kb on + strand, within BPHYT_RS18505at 4163.073 kb on + strand, within BPHYT_RS18505at 4163.074 kb on - strand, within BPHYT_RS18505at 4163.074 kb on - strand, within BPHYT_RS18505at 4163.074 kb on - strand, within BPHYT_RS18505at 4163.246 kb on - strand, within BPHYT_RS18505at 4163.263 kb on - strand, within BPHYT_RS18505at 4163.670 kb on + strand, within BPHYT_RS18505at 4163.671 kb on - strand, within BPHYT_RS18505at 4163.736 kb on + strand, within BPHYT_RS18505at 4163.736 kb on + strand, within BPHYT_RS18505at 4163.736 kb on + strand, within BPHYT_RS18505at 4163.736 kb on + strand, within BPHYT_RS18505at 4163.737 kb on - strand, within BPHYT_RS18505at 4163.751 kb on + strand, within BPHYT_RS18505at 4163.785 kb on + strand, within BPHYT_RS18505at 4163.785 kb on + strand, within BPHYT_RS18505at 4163.786 kb on - strand, within BPHYT_RS18505at 4163.830 kb on - strand, within BPHYT_RS18505at 4163.939 kb on + strand, within BPHYT_RS18505at 4163.940 kb on - strand, within BPHYT_RS18505at 4163.940 kb on - strand, within BPHYT_RS18505at 4163.940 kb on - strand, within BPHYT_RS18505at 4163.940 kb on - strand, within BPHYT_RS18505at 4164.057 kb on - strandat 4164.156 kb on + strandat 4164.190 kb on - strandat 4164.190 kb on - strandat 4164.204 kb on + strandat 4164.204 kb on + strandat 4164.205 kb on - strandat 4164.205 kb on - strandat 4164.298 kb on - strand, within BPHYT_RS18510at 4164.304 kb on + strand, within BPHYT_RS18510at 4164.304 kb on + strand, within BPHYT_RS18510at 4164.305 kb on - strand, within BPHYT_RS18510at 4164.305 kb on - strand, within BPHYT_RS18510at 4164.305 kb on - strand, within BPHYT_RS18510at 4164.320 kb on + strand, within BPHYT_RS18510at 4164.445 kb on - strand, within BPHYT_RS18510at 4164.583 kb on + strandat 4164.583 kb on + strandat 4164.583 kb on + strandat 4164.603 kb on + strandat 4164.603 kb on + strandat 4164.603 kb on + strandat 4164.604 kb on - strandat 4164.608 kb on + strand, within BPHYT_RS18515at 4164.609 kb on - strand, within BPHYT_RS18515at 4164.890 kb on + strandat 4164.891 kb on - strandat 4164.891 kb on - strandat 4164.891 kb on - strandat 4164.902 kb on + strandat 4164.976 kb on + strandat 4165.016 kb on - strandat 4165.016 kb on - strandat 4165.016 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Plant=switchgrass; PlantTreatment=high_phosphate; Sample=rhizosphere; GrowthSubstrate=Agar_0.5%; Collection=LB_with_kan50; Time=3weeks; NumberPlantsPooled=10
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4,162,018 + BPHYT_RS18500 0.37 -0.8
4,162,100 - BPHYT_RS18500 0.46 +0.1
4,162,100 - BPHYT_RS18500 0.46 +0.5
4,162,149 + BPHYT_RS18500 0.52 +1.6
4,162,149 + BPHYT_RS18500 0.52 +1.6
4,162,149 + BPHYT_RS18500 0.52 +0.5
4,162,150 - BPHYT_RS18500 0.52 -1.5
4,162,150 - BPHYT_RS18500 0.52 -0.8
4,162,327 - BPHYT_RS18500 0.71 -1.6
4,162,359 - BPHYT_RS18500 0.75 +0.4
4,162,389 + BPHYT_RS18500 0.78 -1.4
4,162,390 - BPHYT_RS18500 0.78 +1.0
4,162,458 - BPHYT_RS18500 0.86 +1.1
4,162,458 - BPHYT_RS18500 0.86 -0.7
4,162,465 + BPHYT_RS18500 0.86 -0.0
4,162,466 - BPHYT_RS18500 0.87 -0.7
4,162,466 - BPHYT_RS18500 0.87 +1.1
4,162,534 + -2.3
4,162,535 - +0.3
4,162,577 - -0.4
4,162,701 + -1.6
4,162,771 + -0.5
4,162,772 - +1.5
4,162,797 + +0.5
4,162,798 - -0.4
4,162,866 - -0.2
4,162,971 + -1.2
4,162,993 - -1.4
4,162,993 - -1.3
4,163,005 + -2.9
4,163,067 + BPHYT_RS18505 0.12 -1.0
4,163,068 - BPHYT_RS18505 0.12 -2.7
4,163,068 - -0.5
4,163,073 + BPHYT_RS18505 0.12 -1.1
4,163,073 + BPHYT_RS18505 0.12 -0.5
4,163,073 + BPHYT_RS18505 0.12 -1.3
4,163,074 - BPHYT_RS18505 0.12 -2.6
4,163,074 - BPHYT_RS18505 0.12 -2.4
4,163,074 - BPHYT_RS18505 0.12 -1.6
4,163,246 - BPHYT_RS18505 0.26 -0.8
4,163,263 - BPHYT_RS18505 0.28 -0.9
4,163,670 + BPHYT_RS18505 0.61 -0.8
4,163,671 - BPHYT_RS18505 0.61 +0.2
4,163,736 + BPHYT_RS18505 0.66 -1.3
4,163,736 + BPHYT_RS18505 0.66 -1.2
4,163,736 + BPHYT_RS18505 0.66 -0.5
4,163,736 + BPHYT_RS18505 0.66 -0.3
4,163,737 - BPHYT_RS18505 0.66 -2.0
4,163,751 + BPHYT_RS18505 0.67 +1.1
4,163,785 + BPHYT_RS18505 0.70 +0.3
4,163,785 + BPHYT_RS18505 0.70 +0.1
4,163,786 - BPHYT_RS18505 0.70 -0.2
4,163,830 - BPHYT_RS18505 0.74 -2.1
4,163,939 + BPHYT_RS18505 0.83 -0.8
4,163,940 - BPHYT_RS18505 0.83 -0.7
4,163,940 - BPHYT_RS18505 0.83 -0.7
4,163,940 - BPHYT_RS18505 0.83 -0.3
4,163,940 - BPHYT_RS18505 0.83 -1.0
4,164,057 - -0.6
4,164,156 + -0.5
4,164,190 - -1.9
4,164,190 - +0.8
4,164,204 + -1.4
4,164,204 + -0.7
4,164,205 - +0.1
4,164,205 - +1.2
4,164,298 - BPHYT_RS18510 0.19 +0.0
4,164,304 + BPHYT_RS18510 0.20 +0.0
4,164,304 + BPHYT_RS18510 0.20 -0.1
4,164,305 - BPHYT_RS18510 0.21 -0.6
4,164,305 - BPHYT_RS18510 0.21 +1.1
4,164,305 - BPHYT_RS18510 0.21 +0.7
4,164,320 + BPHYT_RS18510 0.25 +0.4
4,164,445 - BPHYT_RS18510 0.60 +2.4
4,164,583 + +0.8
4,164,583 + -1.7
4,164,583 + -0.8
4,164,603 + -0.7
4,164,603 + +0.2
4,164,603 + +0.3
4,164,604 - -1.4
4,164,608 + BPHYT_RS18515 0.11 +0.3
4,164,609 - BPHYT_RS18515 0.11 +0.7
4,164,890 + -0.9
4,164,891 - -0.3
4,164,891 - -0.6
4,164,891 - +1.7
4,164,902 + +0.0
4,164,976 + +0.2
4,165,016 - -0.1
4,165,016 - -0.3
4,165,016 - -0.1

Or see this region's nucleotide sequence