Strain Fitness in Pseudomonas putida KT2440 around PP_1570

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs

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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 ntPP_1567 and PP_1568 are separated by 41 nucleotidesPP_1568 and PP_1569 are separated by 3 nucleotidesPP_1569 and PP_1570 overlap by 1 nucleotidesPP_1570 and PP_1571 overlap by 8 nucleotidesPP_1571 and PP_1572 overlap by 4 nucleotidesPP_1572 and PP_1573 are separated by 65 nucleotides PP_1567: PP_1567 - Capsid protein, at 1,760,853 to 1,762,097 _1567 PP_1568: PP_1568 - conserved protein of unknown function, at 1,762,139 to 1,762,363 _1568 PP_1569: PP_1569 - conserved protein of unknown function, at 1,762,367 to 1,762,843 _1569 PP_1570: PP_1570 - Head-tail adaptor, at 1,762,843 to 1,763,184 _1570 PP_1571: PP_1571 - conserved protein of unknown function, at 1,763,177 to 1,763,662 _1571 PP_1572: PP_1572 - conserved protein of unknown function, at 1,763,659 to 1,764,027 _1572 PP_1573: PP_1573 - putative Major tail protein, at 1,764,093 to 1,764,827 _1573 Position (kb) 1762 1763 1764Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 1761.854 kb on - strand, within PP_1567at 1762.139 kb on - strandat 1762.191 kb on - strand, within PP_1568at 1762.366 kb on + strandat 1762.366 kb on + strandat 1762.366 kb on + strandat 1762.366 kb on + strandat 1762.367 kb on - strandat 1762.367 kb on - strandat 1762.367 kb on - strandat 1762.367 kb on - strandat 1762.551 kb on + strand, within PP_1569at 1762.658 kb on + strand, within PP_1569at 1762.658 kb on + strand, within PP_1569at 1762.659 kb on - strand, within PP_1569at 1762.683 kb on - strand, within PP_1569at 1762.696 kb on + strand, within PP_1569at 1762.696 kb on + strand, within PP_1569at 1763.057 kb on + strand, within PP_1570at 1763.058 kb on - strand, within PP_1570at 1763.095 kb on + strand, within PP_1570at 1763.095 kb on + strand, within PP_1570at 1763.096 kb on - strand, within PP_1570at 1763.096 kb on - strand, within PP_1570at 1763.153 kb on + strandat 1763.153 kb on + strandat 1763.154 kb on - strandat 1763.154 kb on - strandat 1763.505 kb on + strand, within PP_1571at 1763.546 kb on - strand, within PP_1571at 1763.588 kb on - strand, within PP_1571at 1763.604 kb on - strand, within PP_1571at 1763.741 kb on - strand, within PP_1572at 1763.779 kb on + strand, within PP_1572at 1763.779 kb on + strand, within PP_1572at 1763.780 kb on - strand, within PP_1572at 1763.780 kb on - strand, within PP_1572at 1763.819 kb on - strand, within PP_1572at 1763.819 kb on - strand, within PP_1572at 1763.938 kb on + strand, within PP_1572at 1763.938 kb on + strand, within PP_1572at 1763.938 kb on + strand, within PP_1572at 1763.938 kb on + strand, within PP_1572at 1763.938 kb on + strand, within PP_1572at 1763.939 kb on - strand, within PP_1572at 1763.987 kb on - strand, within PP_1572at 1764.046 kb on + strandat 1764.123 kb on + strandat 1764.123 kb on + strandat 1764.123 kb on + strandat 1764.124 kb on - strandat 1764.153 kb on - strandat 1764.157 kb on + strandat 1764.157 kb on + strandat 1764.157 kb on + strandat 1764.158 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=72_hrs
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1,761,854 - PP_1567 0.80 +0.5
1,762,139 - +0.3
1,762,191 - PP_1568 0.23 -1.2
1,762,366 + -0.2
1,762,366 + -1.9
1,762,366 + +0.6
1,762,366 + -0.4
1,762,367 - +2.6
1,762,367 - +0.2
1,762,367 - +0.3
1,762,367 - +2.1
1,762,551 + PP_1569 0.39 -0.1
1,762,658 + PP_1569 0.61 -0.3
1,762,658 + PP_1569 0.61 -0.1
1,762,659 - PP_1569 0.61 -0.1
1,762,683 - PP_1569 0.66 +1.5
1,762,696 + PP_1569 0.69 -0.9
1,762,696 + PP_1569 0.69 -0.5
1,763,057 + PP_1570 0.63 +2.8
1,763,058 - PP_1570 0.63 +0.7
1,763,095 + PP_1570 0.74 +0.9
1,763,095 + PP_1570 0.74 +0.3
1,763,096 - PP_1570 0.74 -1.7
1,763,096 - PP_1570 0.74 +2.3
1,763,153 + +0.2
1,763,153 + +1.2
1,763,154 - +0.8
1,763,154 - -0.2
1,763,505 + PP_1571 0.67 +0.5
1,763,546 - PP_1571 0.76 +0.6
1,763,588 - PP_1571 0.85 -0.4
1,763,604 - PP_1571 0.88 -0.5
1,763,741 - PP_1572 0.22 +0.1
1,763,779 + PP_1572 0.33 -0.3
1,763,779 + PP_1572 0.33 -0.5
1,763,780 - PP_1572 0.33 +1.1
1,763,780 - PP_1572 0.33 -0.8
1,763,819 - PP_1572 0.43 +0.6
1,763,819 - PP_1572 0.43 +0.3
1,763,938 + PP_1572 0.76 +1.3
1,763,938 + PP_1572 0.76 +0.4
1,763,938 + PP_1572 0.76 -2.8
1,763,938 + PP_1572 0.76 +0.4
1,763,938 + PP_1572 0.76 -0.6
1,763,939 - PP_1572 0.76 +0.7
1,763,987 - PP_1572 0.89 +1.1
1,764,046 + -1.0
1,764,123 + -0.8
1,764,123 + +0.1
1,764,123 + -0.4
1,764,124 - -0.9
1,764,153 - +0.3
1,764,157 + +1.0
1,764,157 + +0.3
1,764,157 + +0.1
1,764,158 - -0.7

Or see this region's nucleotide sequence