Strain Fitness in Shewanella oneidensis MR-1 around SO0905

Experiment: Choline chloride 150 mM

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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 ntnqrB-1 and nqrC-1 overlap by 11 nucleotidesnqrC-1 and nqrD-1 overlap by 4 nucleotidesnqrD-1 and nqrE-1 are separated by 9 nucleotidesnqrE-1 and nqrF-1 are separated by 51 nucleotides SO0903: nqrB-1 - NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrB (NCBI ptt file), at 930,300 to 931,532 nqrB-1 SO0904: nqrC-1 - NADH:ubiquinone oxidoreductase, Na translocating, gamma subunit (NCBI ptt file), at 931,522 to 932,316 nqrC-1 SO0905: nqrD-1 - NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrD (NCBI ptt file), at 932,313 to 932,933 nqrD-1 SO0906: nqrE-1 - NADH:ubiquinone oxidoreductase, Na translocating, hydrophobic membrane protein NqrE (NCBI ptt file), at 932,943 to 933,551 nqrE-1 SO0907: nqrF-1 - NADH:ubiquinone oxidoreductase, Na translocating, beta subunit (NCBI ptt file), at 933,603 to 934,820 nqrF-1 Position (kb) 932 933Strain fitness (log2 ratio) -2 -1 0 1 2at 931.428 kb on + strandat 931.457 kb on + strandat 931.465 kb on - strandat 931.565 kb on + strandat 931.589 kb on + strandat 931.589 kb on + strandat 931.589 kb on + strandat 931.597 kb on - strandat 931.597 kb on - strandat 931.624 kb on - strand, within nqrC-1at 931.770 kb on - strand, within nqrC-1at 931.801 kb on - strand, within nqrC-1at 931.811 kb on - strand, within nqrC-1at 931.838 kb on + strand, within nqrC-1at 931.838 kb on - strand, within nqrC-1at 931.889 kb on + strand, within nqrC-1at 931.890 kb on + strand, within nqrC-1at 931.899 kb on - strand, within nqrC-1at 932.045 kb on - strand, within nqrC-1at 932.075 kb on + strand, within nqrC-1at 932.136 kb on + strand, within nqrC-1at 932.298 kb on + strandat 932.306 kb on - strandat 932.385 kb on + strand, within nqrD-1at 932.414 kb on + strand, within nqrD-1at 932.427 kb on - strand, within nqrD-1at 932.446 kb on + strand, within nqrD-1at 932.510 kb on + strand, within nqrD-1at 932.510 kb on + strand, within nqrD-1at 932.652 kb on + strand, within nqrD-1at 932.660 kb on - strand, within nqrD-1at 932.664 kb on + strand, within nqrD-1at 932.684 kb on + strand, within nqrD-1at 932.700 kb on + strand, within nqrD-1at 932.708 kb on - strand, within nqrD-1at 932.737 kb on + strand, within nqrD-1at 932.737 kb on + strand, within nqrD-1at 932.745 kb on - strand, within nqrD-1at 932.745 kb on - strand, within nqrD-1at 932.790 kb on - strand, within nqrD-1at 932.805 kb on - strand, within nqrD-1at 932.805 kb on - strand, within nqrD-1at 932.927 kb on + strandat 932.961 kb on - strandat 932.961 kb on - strandat 932.970 kb on - strandat 932.979 kb on + strandat 932.980 kb on - strandat 932.997 kb on - strandat 932.999 kb on + strandat 933.015 kb on + strand, within nqrE-1at 933.023 kb on - strand, within nqrE-1at 933.025 kb on + strand, within nqrE-1at 933.035 kb on + strand, within nqrE-1at 933.138 kb on - strand, within nqrE-1at 933.157 kb on - strand, within nqrE-1at 933.157 kb on - strand, within nqrE-1at 933.157 kb on - strand, within nqrE-1at 933.259 kb on + strand, within nqrE-1at 933.311 kb on - strand, within nqrE-1at 933.407 kb on - strand, within nqrE-1at 933.407 kb on - strand, within nqrE-1at 933.407 kb on - strand, within nqrE-1at 933.425 kb on + strand, within nqrE-1at 933.430 kb on - strand, within nqrE-1at 933.468 kb on + strand, within nqrE-1at 933.469 kb on + strand, within nqrE-1at 933.469 kb on + strand, within nqrE-1at 933.477 kb on - strand, within nqrE-1at 933.486 kb on - strand, within nqrE-1at 933.513 kb on + strandat 933.557 kb on + strandat 933.634 kb on + strandat 933.647 kb on - strandat 933.701 kb on + strandat 933.828 kb on + strand, within nqrF-1

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Per-strain Table

Position Strand Gene LocusTag Fraction Choline chloride 150 mM
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931,428 + -0.4
931,457 + -0.1
931,465 - +0.5
931,565 + +0.8
931,589 + -0.1
931,589 + +0.8
931,589 + +0.5
931,597 - +0.3
931,597 - +0.8
931,624 - nqrC-1 SO0904 0.13 -0.1
931,770 - nqrC-1 SO0904 0.31 -1.1
931,801 - nqrC-1 SO0904 0.35 +0.1
931,811 - nqrC-1 SO0904 0.36 +1.2
931,838 + nqrC-1 SO0904 0.40 -0.9
931,838 - nqrC-1 SO0904 0.40 -0.7
931,889 + nqrC-1 SO0904 0.46 +0.7
931,890 + nqrC-1 SO0904 0.46 -0.3
931,899 - nqrC-1 SO0904 0.47 +0.2
932,045 - nqrC-1 SO0904 0.66 +0.0
932,075 + nqrC-1 SO0904 0.70 +1.0
932,136 + nqrC-1 SO0904 0.77 +0.4
932,298 + +0.6
932,306 - -0.0
932,385 + nqrD-1 SO0905 0.12 +0.0
932,414 + nqrD-1 SO0905 0.16 +0.0
932,427 - nqrD-1 SO0905 0.18 +0.3
932,446 + nqrD-1 SO0905 0.21 -0.3
932,510 + nqrD-1 SO0905 0.32 -0.4
932,510 + nqrD-1 SO0905 0.32 +0.2
932,652 + nqrD-1 SO0905 0.55 +0.1
932,660 - nqrD-1 SO0905 0.56 +0.2
932,664 + nqrD-1 SO0905 0.57 +0.0
932,684 + nqrD-1 SO0905 0.60 -0.6
932,700 + nqrD-1 SO0905 0.62 -1.1
932,708 - nqrD-1 SO0905 0.64 -0.3
932,737 + nqrD-1 SO0905 0.68 -0.7
932,737 + nqrD-1 SO0905 0.68 +0.5
932,745 - nqrD-1 SO0905 0.70 +1.8
932,745 - nqrD-1 SO0905 0.70 -1.1
932,790 - nqrD-1 SO0905 0.77 -1.0
932,805 - nqrD-1 SO0905 0.79 +0.1
932,805 - nqrD-1 SO0905 0.79 +0.2
932,927 + -0.3
932,961 - -1.0
932,961 - -0.2
932,970 - -0.3
932,979 + +1.0
932,980 - +0.3
932,997 - -1.2
932,999 + +1.0
933,015 + nqrE-1 SO0906 0.12 +0.2
933,023 - nqrE-1 SO0906 0.13 +0.4
933,025 + nqrE-1 SO0906 0.13 +0.4
933,035 + nqrE-1 SO0906 0.15 -0.5
933,138 - nqrE-1 SO0906 0.32 -1.3
933,157 - nqrE-1 SO0906 0.35 -0.2
933,157 - nqrE-1 SO0906 0.35 +0.4
933,157 - nqrE-1 SO0906 0.35 -0.1
933,259 + nqrE-1 SO0906 0.52 +0.2
933,311 - nqrE-1 SO0906 0.60 -0.9
933,407 - nqrE-1 SO0906 0.76 +1.0
933,407 - nqrE-1 SO0906 0.76 -0.2
933,407 - nqrE-1 SO0906 0.76 +0.6
933,425 + nqrE-1 SO0906 0.79 +0.9
933,430 - nqrE-1 SO0906 0.80 -0.5
933,468 + nqrE-1 SO0906 0.86 -0.2
933,469 + nqrE-1 SO0906 0.86 -1.1
933,469 + nqrE-1 SO0906 0.86 -2.0
933,477 - nqrE-1 SO0906 0.88 -0.9
933,486 - nqrE-1 SO0906 0.89 -0.5
933,513 + +0.8
933,557 + -0.0
933,634 + +0.5
933,647 - +2.3
933,701 + -1.3
933,828 + nqrF-1 SO0907 0.18 -0.3

Or see this region's nucleotide sequence