Strain Fitness in Burkholderia phytofirmans PsJN around BPHYT_RS02905

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_RS02895 and BPHYT_RS02900 are separated by 337 nucleotidesBPHYT_RS02900 and BPHYT_RS02905 are separated by 170 nucleotidesBPHYT_RS02905 and BPHYT_RS02910 are separated by 187 nucleotidesBPHYT_RS02910 and BPHYT_RS02915 overlap by 4 nucleotides BPHYT_RS02895: BPHYT_RS02895 - PTS sugar transporter subunit IIA, at 645,072 to 645,527 _RS02895 BPHYT_RS02900: BPHYT_RS02900 - ribosome hibernation promoting factor, at 645,865 to 646,221 _RS02900 BPHYT_RS02905: BPHYT_RS02905 - RNA polymerase subunit sigma-54, at 646,392 to 647,903 _RS02905 BPHYT_RS02910: BPHYT_RS02910 - ABC transporter, at 648,091 to 648,876 _RS02910 BPHYT_RS02915: BPHYT_RS02915 - organic solvent tolerance protein OstA, at 648,873 to 649,544 _RS02915 Position (kb) 646 647 648Strain fitness (log2 ratio) -8 -7 -6 -5 -4 -3 -2 -1 0 1at 645.663 kb on + strandat 645.691 kb on + strandat 645.691 kb on + strandat 645.692 kb on - strandat 645.692 kb on - strandat 645.692 kb on - strandat 645.692 kb on - strandat 645.693 kb on + strandat 645.693 kb on + strandat 645.693 kb on + strandat 645.694 kb on - strandat 645.694 kb on - strandat 645.736 kb on + strandat 645.884 kb on - strandat 645.902 kb on + strand, within BPHYT_RS02900at 645.903 kb on - strand, within BPHYT_RS02900at 645.996 kb on - strand, within BPHYT_RS02900at 646.139 kb on - strand, within BPHYT_RS02900at 646.186 kb on + strandat 646.221 kb on + strandat 646.221 kb on + strandat 646.237 kb on + strandat 646.237 kb on + strandat 646.238 kb on - strandat 646.238 kb on - strandat 646.265 kb on + strandat 646.266 kb on - strandat 646.266 kb on - strandat 646.266 kb on - strandat 646.365 kb on + strandat 646.393 kb on + strandat 646.394 kb on - strandat 646.442 kb on - strandat 646.455 kb on - strandat 646.540 kb on - strandat 646.553 kb on + strand, within BPHYT_RS02905at 646.554 kb on - strand, within BPHYT_RS02905at 646.621 kb on + strand, within BPHYT_RS02905at 646.625 kb on + strand, within BPHYT_RS02905at 646.626 kb on - strand, within BPHYT_RS02905at 646.657 kb on + strand, within BPHYT_RS02905at 646.657 kb on + strandat 646.658 kb on - strand, within BPHYT_RS02905at 646.658 kb on - strand, within BPHYT_RS02905at 646.658 kb on - strand, within BPHYT_RS02905at 646.658 kb on - strand, within BPHYT_RS02905at 646.706 kb on + strand, within BPHYT_RS02905at 646.707 kb on - strand, within BPHYT_RS02905at 646.707 kb on - strand, within BPHYT_RS02905at 646.707 kb on - strand, within BPHYT_RS02905at 646.895 kb on + strand, within BPHYT_RS02905at 646.916 kb on - strand, within BPHYT_RS02905at 646.916 kb on - strand, within BPHYT_RS02905at 646.925 kb on + strand, within BPHYT_RS02905at 646.929 kb on - strand, within BPHYT_RS02905at 646.929 kb on - strand, within BPHYT_RS02905at 647.011 kb on + strand, within BPHYT_RS02905at 647.011 kb on + strand, within BPHYT_RS02905at 647.011 kb on + strand, within BPHYT_RS02905at 647.011 kb on + strand, within BPHYT_RS02905at 647.011 kb on + strand, within BPHYT_RS02905at 647.012 kb on - strand, within BPHYT_RS02905at 647.012 kb on - strand, within BPHYT_RS02905at 647.070 kb on + strand, within BPHYT_RS02905at 647.070 kb on + strand, within BPHYT_RS02905at 647.070 kb on + strand, within BPHYT_RS02905at 647.070 kb on + strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.071 kb on - strand, within BPHYT_RS02905at 647.172 kb on + strand, within BPHYT_RS02905at 647.189 kb on + strand, within BPHYT_RS02905at 647.270 kb on + strand, within BPHYT_RS02905at 647.270 kb on + strand, within BPHYT_RS02905at 647.271 kb on - strand, within BPHYT_RS02905at 647.271 kb on - strand, within BPHYT_RS02905at 647.365 kb on + strand, within BPHYT_RS02905at 647.366 kb on - strand, within BPHYT_RS02905at 647.536 kb on + strand, within BPHYT_RS02905at 647.593 kb on + strand, within BPHYT_RS02905at 647.594 kb on - strand, within BPHYT_RS02905at 647.654 kb on + strand, within BPHYT_RS02905at 647.654 kb on + strand, within BPHYT_RS02905at 647.655 kb on - strand, within BPHYT_RS02905at 647.655 kb on - strand, within BPHYT_RS02905at 647.816 kb on + strandat 647.816 kb on + strandat 647.817 kb on - strandat 647.817 kb on - strandat 647.826 kb on + strandat 647.826 kb on + strandat 647.826 kb on + strandat 647.827 kb on - strandat 647.827 kb on - strandat 647.827 kb on - strandat 647.923 kb on + strandat 647.947 kb on - strandat 647.966 kb on + strandat 647.966 kb on + strandat 648.092 kb on + strandat 648.092 kb on + strandat 648.092 kb on + strandat 648.092 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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645,663 + -0.2
645,691 + -2.7
645,691 + +0.4
645,692 - +0.2
645,692 - -0.1
645,692 - +0.5
645,692 - -0.5
645,693 + -0.6
645,693 + -0.4
645,693 + -1.1
645,694 - -2.2
645,694 - +1.0
645,736 + -0.9
645,884 - +0.2
645,902 + BPHYT_RS02900 0.10 -0.3
645,903 - BPHYT_RS02900 0.11 -2.0
645,996 - BPHYT_RS02900 0.37 -0.1
646,139 - BPHYT_RS02900 0.77 -2.6
646,186 + -0.8
646,221 + -0.2
646,221 + +0.8
646,237 + -1.3
646,237 + -2.7
646,238 - +0.2
646,238 - +1.4
646,265 + -1.3
646,266 - +0.1
646,266 - +0.4
646,266 - -2.3
646,365 + -1.0
646,393 + -0.4
646,394 - -0.2
646,442 - -3.0
646,455 - -3.4
646,540 - -6.0
646,553 + BPHYT_RS02905 0.11 -3.1
646,554 - BPHYT_RS02905 0.11 -7.7
646,621 + BPHYT_RS02905 0.15 -1.6
646,625 + BPHYT_RS02905 0.15 -2.2
646,626 - BPHYT_RS02905 0.15 -2.1
646,657 + BPHYT_RS02905 0.18 -4.5
646,657 + +0.0
646,658 - BPHYT_RS02905 0.18 -3.1
646,658 - BPHYT_RS02905 0.18 -4.1
646,658 - BPHYT_RS02905 0.18 -3.8
646,658 - BPHYT_RS02905 0.18 -5.6
646,706 + BPHYT_RS02905 0.21 -3.4
646,707 - BPHYT_RS02905 0.21 -7.0
646,707 - BPHYT_RS02905 0.21 -1.7
646,707 - BPHYT_RS02905 0.21 -4.8
646,895 + BPHYT_RS02905 0.33 -2.9
646,916 - BPHYT_RS02905 0.35 -4.0
646,916 - BPHYT_RS02905 0.35 -3.6
646,925 + BPHYT_RS02905 0.35 -3.8
646,929 - BPHYT_RS02905 0.36 -4.9
646,929 - BPHYT_RS02905 0.36 -6.2
647,011 + BPHYT_RS02905 0.41 -2.2
647,011 + BPHYT_RS02905 0.41 -6.0
647,011 + BPHYT_RS02905 0.41 -4.4
647,011 + BPHYT_RS02905 0.41 -5.7
647,011 + BPHYT_RS02905 0.41 -4.9
647,012 - BPHYT_RS02905 0.41 -5.0
647,012 - BPHYT_RS02905 0.41 -2.3
647,070 + BPHYT_RS02905 0.45 -2.5
647,070 + BPHYT_RS02905 0.45 -4.8
647,070 + BPHYT_RS02905 0.45 -3.1
647,070 + BPHYT_RS02905 0.45 -8.0
647,071 - BPHYT_RS02905 0.45 -2.9
647,071 - BPHYT_RS02905 0.45 -5.1
647,071 - BPHYT_RS02905 0.45 -5.0
647,071 - BPHYT_RS02905 0.45 -8.3
647,071 - BPHYT_RS02905 0.45 -3.9
647,071 - BPHYT_RS02905 0.45 -5.2
647,172 + BPHYT_RS02905 0.52 -4.7
647,189 + BPHYT_RS02905 0.53 -4.6
647,270 + BPHYT_RS02905 0.58 -3.8
647,270 + BPHYT_RS02905 0.58 -0.2
647,271 - BPHYT_RS02905 0.58 -4.0
647,271 - BPHYT_RS02905 0.58 -5.2
647,365 + BPHYT_RS02905 0.64 -5.3
647,366 - BPHYT_RS02905 0.64 -4.3
647,536 + BPHYT_RS02905 0.76 -1.1
647,593 + BPHYT_RS02905 0.79 -3.8
647,594 - BPHYT_RS02905 0.79 -3.6
647,654 + BPHYT_RS02905 0.83 -7.7
647,654 + BPHYT_RS02905 0.83 -3.3
647,655 - BPHYT_RS02905 0.84 -4.0
647,655 - BPHYT_RS02905 0.84 -6.0
647,816 + -3.5
647,816 + -4.8
647,817 - -1.2
647,817 - -1.4
647,826 + -2.3
647,826 + -2.9
647,826 + -6.4
647,827 - -3.2
647,827 - -5.2
647,827 - -6.1
647,923 + -0.1
647,947 - +0.4
647,966 + +0.2
647,966 + -2.8
648,092 + +0.1
648,092 + +0.1
648,092 + +1.0
648,092 + -0.1

Or see this region's nucleotide sequence