Strain Fitness in Pseudomonas putida KT2440 around PP_1687

Experiment: Soil=PNNL_Prosser_PlotA_B_20191220; Sterility=nonsterile; Collection=outgrowth_in_LB_2hrs_then_extra_outgrowth_in_LB; SoilTreatment=none; SoilTreatmentTime=288_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_1684 and PP_1685 overlap by 4 nucleotidesPP_1685 and PP_1686 overlap by 11 nucleotidesPP_1686 and PP_1687 are separated by 135 nucleotidesPP_1687 and PP_1688 are separated by 75 nucleotides PP_1684: PP_1684 - putative Transporter, at 1,877,879 to 1,879,099 _1684 PP_1685: PP_1685 - conserved exported protein of unknown function, at 1,879,096 to 1,879,218 _1685 PP_1686: PP_1686 - Glutathione peroxidase, at 1,879,208 to 1,879,816 _1686 PP_1687: PP_1687 - conserved exported protein of unknown function, at 1,879,952 to 1,880,251 _1687 PP_1688: PP_1688 - Transcriptional regulator, LysR family, at 1,880,327 to 1,881,256 _1688 Position (kb) 1879 1880 1881Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 1878.975 kb on - strand, within PP_1684at 1878.975 kb on - strand, within PP_1684at 1878.975 kb on - strand, within PP_1684at 1878.975 kb on - strand, within PP_1684at 1878.975 kb on - strand, within PP_1684at 1878.992 kb on + strandat 1878.992 kb on + strandat 1878.992 kb on + strandat 1878.992 kb on + strandat 1878.993 kb on - strandat 1878.993 kb on - strandat 1879.046 kb on - strandat 1879.095 kb on + strandat 1879.095 kb on + strandat 1879.096 kb on - strandat 1879.096 kb on - strandat 1879.105 kb on + strandat 1879.106 kb on - strandat 1879.128 kb on + strand, within PP_1685at 1879.216 kb on + strandat 1879.312 kb on + strand, within PP_1686at 1879.313 kb on - strand, within PP_1686at 1879.442 kb on + strand, within PP_1686at 1879.443 kb on - strand, within PP_1686at 1879.484 kb on + strand, within PP_1686at 1879.484 kb on + strand, within PP_1686at 1879.485 kb on - strand, within PP_1686at 1879.485 kb on - strand, within PP_1686at 1879.485 kb on - strand, within PP_1686at 1879.485 kb on - strand, within PP_1686at 1879.493 kb on + strand, within PP_1686at 1879.493 kb on + strand, within PP_1686at 1879.494 kb on - strand, within PP_1686at 1879.584 kb on - strand, within PP_1686at 1879.592 kb on + strand, within PP_1686at 1879.592 kb on + strand, within PP_1686at 1879.592 kb on + strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.593 kb on - strand, within PP_1686at 1879.700 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.706 kb on + strand, within PP_1686at 1879.707 kb on - strand, within PP_1686at 1879.707 kb on - strand, within PP_1686at 1879.707 kb on - strand, within PP_1686at 1879.970 kb on - strandat 1879.973 kb on - strandat 1880.043 kb on + strand, within PP_1687at 1880.044 kb on - strand, within PP_1687at 1880.067 kb on + strand, within PP_1687at 1880.067 kb on + strand, within PP_1687at 1880.067 kb on + strand, within PP_1687at 1880.067 kb on + strand, within PP_1687at 1880.067 kb on + strand, within PP_1687at 1880.068 kb on - strand, within PP_1687at 1880.068 kb on - strand, within PP_1687at 1880.068 kb on - strand, within PP_1687at 1880.068 kb on - strand, within PP_1687at 1880.068 kb on - strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.139 kb on + strand, within PP_1687at 1880.140 kb on - strand, within PP_1687at 1880.140 kb on - strand, within PP_1687at 1880.155 kb on - strand, within PP_1687at 1880.179 kb on + strand, within PP_1687at 1880.246 kb on + strandat 1880.263 kb on - strandat 1880.270 kb on + strandat 1880.271 kb on - strandat 1880.295 kb on + strandat 1880.295 kb on + strandat 1880.347 kb on + strandat 1880.377 kb on + strandat 1880.378 kb on - strandat 1880.463 kb on + strand, within PP_1688at 1880.519 kb on + strand, within PP_1688at 1880.519 kb on + strand, within PP_1688at 1880.520 kb on - strand, within PP_1688at 1880.520 kb on - strand, within PP_1688at 1880.522 kb on + strand, within PP_1688at 1880.523 kb on - strand, within PP_1688at 1880.523 kb on - strand, within PP_1688at 1880.532 kb on + strand, within PP_1688at 1880.533 kb on - strand, within PP_1688at 1880.540 kb on - strand, within PP_1688at 1880.540 kb on - strand, within PP_1688at 1880.658 kb on + strand, within PP_1688at 1880.722 kb on + strand, within PP_1688at 1880.856 kb on + strand, within PP_1688at 1880.982 kb on + strand, within PP_1688at 1880.982 kb on + strand, within PP_1688at 1880.982 kb on + strand, within PP_1688at 1880.982 kb on + strand, within PP_1688at 1880.983 kb on - strand, within PP_1688at 1880.983 kb on - strand, within PP_1688at 1881.122 kb on + strand, within PP_1688at 1881.149 kb on + strand, within PP_1688at 1881.155 kb on + strandat 1881.155 kb on + strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.156 kb on - strand, within PP_1688at 1881.213 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=288_hrs
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1,878,975 - PP_1684 0.90 -0.4
1,878,975 - PP_1684 0.90 +0.4
1,878,975 - PP_1684 0.90 -0.3
1,878,975 - PP_1684 0.90 -0.9
1,878,975 - PP_1684 0.90 -2.0
1,878,992 + -1.5
1,878,992 + -1.5
1,878,992 + +0.2
1,878,992 + -0.5
1,878,993 - -0.4
1,878,993 - -0.7
1,879,046 - +1.0
1,879,095 + -0.0
1,879,095 + +0.5
1,879,096 - +1.4
1,879,096 - +0.3
1,879,105 + -0.9
1,879,106 - +1.3
1,879,128 + PP_1685 0.26 +0.5
1,879,216 + -1.0
1,879,312 + PP_1686 0.17 +0.0
1,879,313 - PP_1686 0.17 -0.6
1,879,442 + PP_1686 0.38 +0.6
1,879,443 - PP_1686 0.39 -0.9
1,879,484 + PP_1686 0.45 -0.1
1,879,484 + PP_1686 0.45 -0.5
1,879,485 - PP_1686 0.45 -2.1
1,879,485 - PP_1686 0.45 -0.1
1,879,485 - PP_1686 0.45 -0.1
1,879,485 - PP_1686 0.45 +0.1
1,879,493 + PP_1686 0.47 +1.2
1,879,493 + PP_1686 0.47 -0.6
1,879,494 - PP_1686 0.47 +0.6
1,879,584 - PP_1686 0.62 +0.6
1,879,592 + PP_1686 0.63 +0.5
1,879,592 + PP_1686 0.63 -0.3
1,879,592 + PP_1686 0.63 +0.4
1,879,593 - PP_1686 0.63 -0.0
1,879,593 - PP_1686 0.63 +0.7
1,879,593 - PP_1686 0.63 +1.1
1,879,593 - PP_1686 0.63 -0.2
1,879,593 - PP_1686 0.63 -0.4
1,879,593 - PP_1686 0.63 -0.3
1,879,593 - PP_1686 0.63 -0.5
1,879,700 + PP_1686 0.81 +1.2
1,879,706 + PP_1686 0.82 +0.9
1,879,706 + PP_1686 0.82 +0.0
1,879,706 + PP_1686 0.82 +0.0
1,879,706 + PP_1686 0.82 +0.8
1,879,706 + PP_1686 0.82 -0.4
1,879,706 + PP_1686 0.82 +0.3
1,879,707 - PP_1686 0.82 +0.6
1,879,707 - PP_1686 0.82 +1.1
1,879,707 - PP_1686 0.82 +0.2
1,879,970 - +0.4
1,879,973 - -3.1
1,880,043 + PP_1687 0.30 +0.1
1,880,044 - PP_1687 0.31 +0.4
1,880,067 + PP_1687 0.38 -1.8
1,880,067 + PP_1687 0.38 +0.8
1,880,067 + PP_1687 0.38 +0.4
1,880,067 + PP_1687 0.38 -0.0
1,880,067 + PP_1687 0.38 +1.2
1,880,068 - PP_1687 0.39 +1.1
1,880,068 - PP_1687 0.39 +1.5
1,880,068 - PP_1687 0.39 +1.3
1,880,068 - PP_1687 0.39 +0.7
1,880,068 - PP_1687 0.39 +1.3
1,880,139 + PP_1687 0.62 +0.1
1,880,139 + PP_1687 0.62 -0.3
1,880,139 + PP_1687 0.62 +0.4
1,880,139 + PP_1687 0.62 +0.4
1,880,139 + PP_1687 0.62 +2.4
1,880,139 + PP_1687 0.62 -0.2
1,880,140 - PP_1687 0.63 +0.5
1,880,140 - PP_1687 0.63 +0.2
1,880,155 - PP_1687 0.68 +0.2
1,880,179 + PP_1687 0.76 +1.1
1,880,246 + -1.0
1,880,263 - -0.8
1,880,270 + -0.1
1,880,271 - +0.8
1,880,295 + +1.3
1,880,295 + +0.3
1,880,347 + +1.0
1,880,377 + -0.3
1,880,378 - +0.5
1,880,463 + PP_1688 0.15 -0.2
1,880,519 + PP_1688 0.21 +0.1
1,880,519 + PP_1688 0.21 +0.5
1,880,520 - PP_1688 0.21 +0.5
1,880,520 - PP_1688 0.21 +1.1
1,880,522 + PP_1688 0.21 -0.5
1,880,523 - PP_1688 0.21 -2.7
1,880,523 - PP_1688 0.21 +0.9
1,880,532 + PP_1688 0.22 +1.4
1,880,533 - PP_1688 0.22 +0.3
1,880,540 - PP_1688 0.23 -0.1
1,880,540 - PP_1688 0.23 +0.3
1,880,658 + PP_1688 0.36 -0.5
1,880,722 + PP_1688 0.42 +0.1
1,880,856 + PP_1688 0.57 -0.4
1,880,982 + PP_1688 0.70 +0.3
1,880,982 + PP_1688 0.70 +0.1
1,880,982 + PP_1688 0.70 +1.2
1,880,982 + PP_1688 0.70 -0.8
1,880,983 - PP_1688 0.71 +0.6
1,880,983 - PP_1688 0.71 +2.0
1,881,122 + PP_1688 0.85 +0.5
1,881,149 + PP_1688 0.88 +0.7
1,881,155 + -0.1
1,881,155 + PP_1688 0.89 -1.4
1,881,156 - PP_1688 0.89 +0.4
1,881,156 - PP_1688 0.89 -0.2
1,881,156 - PP_1688 0.89 +0.3
1,881,156 - PP_1688 0.89 +0.2
1,881,156 - PP_1688 0.89 -0.1
1,881,156 - PP_1688 0.89 -1.1
1,881,156 - PP_1688 0.89 +0.5
1,881,156 - PP_1688 0.89 -0.8
1,881,213 - +0.6

Or see this region's nucleotide sequence