Strain Fitness in Shewanella amazonensis SB2B around Sama_0001

Experiment: benzoic 0.29 mg/ml

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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 ntSama_0001 and Sama_0002 are separated by 146 nucleotides Sama_0001: Sama_0001 - flavodoxin (RefSeq), at 70 to 510 _0001 Sama_0002: Sama_0002 - hypothetical protein (RefSeq), at 657 to 1,571 _0002 Position (kb) 0 1Strain fitness (log2 ratio) -2 -1 0 1 2 3at 0.003 kb on + strandat 0.030 kb on + strandat 0.031 kb on - strandat 0.031 kb on - strandat 0.136 kb on + strand, within Sama_0001at 0.136 kb on + strand, within Sama_0001at 0.137 kb on - strand, within Sama_0001at 0.137 kb on - strand, within Sama_0001at 0.153 kb on + strand, within Sama_0001at 0.187 kb on + strand, within Sama_0001at 0.187 kb on + strand, within Sama_0001at 0.227 kb on + strand, within Sama_0001at 0.227 kb on + strand, within Sama_0001at 0.228 kb on - strand, within Sama_0001at 0.262 kb on + strand, within Sama_0001at 0.263 kb on - strand, within Sama_0001at 0.263 kb on - strand, within Sama_0001at 0.353 kb on - strand, within Sama_0001at 0.353 kb on - strand, within Sama_0001at 0.359 kb on - strand, within Sama_0001at 0.376 kb on - strand, within Sama_0001at 0.437 kb on - strand, within Sama_0001at 0.437 kb on - strand, within Sama_0001at 0.461 kb on + strand, within Sama_0001at 0.461 kb on + strand, within Sama_0001at 0.462 kb on - strand, within Sama_0001at 0.462 kb on - strand, within Sama_0001at 0.462 kb on - strand, within Sama_0001at 0.462 kb on - strand, within Sama_0001at 0.514 kb on + strandat 0.514 kb on + strandat 0.514 kb on + strandat 0.514 kb on + strandat 0.514 kb on + strandat 0.515 kb on - strandat 0.515 kb on - strandat 0.515 kb on - strandat 0.515 kb on - strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.597 kb on + strandat 0.598 kb on - strandat 0.598 kb on - strandat 0.598 kb on - strandat 0.598 kb on - strandat 0.598 kb on - strandat 0.601 kb on + strandat 0.601 kb on + strandat 0.602 kb on - strandat 0.602 kb on - strandat 0.602 kb on - strandat 0.602 kb on - strandat 0.609 kb on + strandat 0.609 kb on + strandat 0.609 kb on + strandat 0.609 kb on + strandat 0.609 kb on + strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.610 kb on - strandat 0.656 kb on + strandat 0.656 kb on + strandat 0.712 kb on + strandat 0.712 kb on + strandat 0.712 kb on + strandat 0.712 kb on + strandat 0.713 kb on - strandat 0.754 kb on + strand, within Sama_0002at 0.754 kb on + strand, within Sama_0002at 0.755 kb on - strand, within Sama_0002at 0.755 kb on - strand, within Sama_0002at 0.783 kb on - strand, within Sama_0002at 0.851 kb on + strand, within Sama_0002at 0.852 kb on - strand, within Sama_0002at 0.852 kb on - strand, within Sama_0002at 0.868 kb on + strand, within Sama_0002at 0.869 kb on - strand, within Sama_0002at 0.920 kb on + strand, within Sama_0002at 0.921 kb on - strand, within Sama_0002at 0.955 kb on + strand, within Sama_0002at 0.955 kb on + strand, within Sama_0002at 0.955 kb on + strand, within Sama_0002at 0.955 kb on + strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.956 kb on - strand, within Sama_0002at 0.961 kb on + strand, within Sama_0002at 0.983 kb on + strand, within Sama_0002at 1.019 kb on + strand, within Sama_0002at 1.028 kb on + strand, within Sama_0002at 1.028 kb on + strand, within Sama_0002at 1.028 kb on + strand, within Sama_0002at 1.029 kb on - strand, within Sama_0002at 1.029 kb on - strand, within Sama_0002at 1.029 kb on - strand, within Sama_0002at 1.029 kb on - strand, within Sama_0002at 1.062 kb on + strand, within Sama_0002at 1.062 kb on + strand, within Sama_0002at 1.063 kb on - strand, within Sama_0002at 1.063 kb on - strand, within Sama_0002at 1.115 kb on - strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.120 kb on + strand, within Sama_0002at 1.164 kb on + strand, within Sama_0002at 1.164 kb on + strand, within Sama_0002at 1.164 kb on + strand, within Sama_0002at 1.164 kb on + strand, within Sama_0002at 1.165 kb on - strand, within Sama_0002at 1.165 kb on - strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.186 kb on + strand, within Sama_0002at 1.187 kb on - strand, within Sama_0002at 1.187 kb on - strand, within Sama_0002at 1.187 kb on - strand, within Sama_0002at 1.187 kb on - strand, within Sama_0002at 1.187 kb on - strand, within Sama_0002at 1.200 kb on - strand, within Sama_0002at 1.200 kb on - strand, within Sama_0002at 1.273 kb on + strand, within Sama_0002at 1.273 kb on + strand, within Sama_0002at 1.274 kb on - strand, within Sama_0002at 1.274 kb on - strand, within Sama_0002at 1.274 kb on - strand, within Sama_0002at 1.313 kb on + strand, within Sama_0002at 1.313 kb on + strand, within Sama_0002at 1.314 kb on - strand, within Sama_0002at 1.384 kb on + strand, within Sama_0002at 1.384 kb on + strand, within Sama_0002at 1.403 kb on + strand, within Sama_0002at 1.403 kb on + strand, within Sama_0002at 1.403 kb on + strand, within Sama_0002at 1.403 kb on + strand, within Sama_0002at 1.404 kb on - strand, within Sama_0002at 1.404 kb on - strand, within Sama_0002at 1.404 kb on - strand, within Sama_0002at 1.404 kb on - strand, within Sama_0002at 1.418 kb on + strand, within Sama_0002at 1.419 kb on - strand, within Sama_0002at 1.419 kb on - strand, within Sama_0002at 1.419 kb on - strand, within Sama_0002at 1.441 kb on - strand, within Sama_0002at 1.450 kb on + strand, within Sama_0002at 1.450 kb on + strand, within Sama_0002at 1.450 kb on + strand, within Sama_0002at 1.450 kb on + strand, within Sama_0002at 1.451 kb on - strand, within Sama_0002at 1.451 kb on - strand, within Sama_0002at 1.451 kb on - strand, within Sama_0002at 1.505 kb on + strandat 1.505 kb on + strandat 1.505 kb on + strandat 1.505 kb on + strandat 1.506 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction benzoic 0.29 mg/ml
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3 + -2.5
30 + +1.2
31 - +0.3
31 - -0.2
136 + Sama_0001 0.15 -1.7
136 + Sama_0001 0.15 -1.1
137 - Sama_0001 0.15 -0.9
137 - Sama_0001 0.15 +0.6
153 + Sama_0001 0.19 -0.5
187 + Sama_0001 0.27 -0.9
187 + Sama_0001 0.27 +0.0
227 + Sama_0001 0.36 +0.5
227 + Sama_0001 0.36 -0.1
228 - Sama_0001 0.36 +0.8
262 + Sama_0001 0.44 -1.1
263 - Sama_0001 0.44 -0.9
263 - Sama_0001 0.44 -0.5
353 - Sama_0001 0.64 +0.5
353 - Sama_0001 0.64 +3.0
359 - Sama_0001 0.66 -1.3
376 - Sama_0001 0.69 -0.9
437 - Sama_0001 0.83 -0.1
437 - Sama_0001 0.83 -0.1
461 + Sama_0001 0.89 -0.4
461 + Sama_0001 0.89 -0.3
462 - Sama_0001 0.89 -0.9
462 - Sama_0001 0.89 -2.5
462 - Sama_0001 0.89 -0.5
462 - Sama_0001 0.89 +0.7
514 + -2.1
514 + -2.2
514 + -0.3
514 + +1.2
514 + -0.9
515 - +0.9
515 - -0.9
515 - -0.3
515 - +0.3
597 + -1.1
597 + +0.1
597 + -0.6
597 + -1.5
597 + +0.0
597 + +0.6
597 + -1.7
598 - +0.9
598 - -1.7
598 - +0.9
598 - +0.3
598 - -0.1
601 + -0.2
601 + +0.4
602 - -0.6
602 - -0.5
602 - +1.5
602 - -0.0
609 + -0.1
609 + -1.4
609 + +0.5
609 + -0.1
609 + -0.4
610 - -0.6
610 - -1.1
610 - +0.6
610 - -1.0
610 - +0.0
610 - -2.2
610 - -0.4
610 - -1.2
656 + +0.5
656 + -0.2
712 + +0.2
712 + -1.3
712 + +0.1
712 + +0.6
713 - -0.0
754 + Sama_0002 0.11 +0.3
754 + Sama_0002 0.11 +0.3
755 - Sama_0002 0.11 +0.5
755 - Sama_0002 0.11 +0.3
783 - Sama_0002 0.14 +0.2
851 + Sama_0002 0.21 -1.5
852 - Sama_0002 0.21 +0.5
852 - Sama_0002 0.21 -0.3
868 + Sama_0002 0.23 -0.0
869 - Sama_0002 0.23 -0.1
920 + Sama_0002 0.29 +0.9
921 - Sama_0002 0.29 +0.5
955 + Sama_0002 0.33 +1.1
955 + Sama_0002 0.33 +0.5
955 + Sama_0002 0.33 +0.4
955 + Sama_0002 0.33 -0.3
956 - Sama_0002 0.33 -0.1
956 - Sama_0002 0.33 -0.7
956 - Sama_0002 0.33 +0.6
956 - Sama_0002 0.33 +0.3
956 - Sama_0002 0.33 +1.5
956 - Sama_0002 0.33 +0.1
956 - Sama_0002 0.33 -0.7
961 + Sama_0002 0.33 -1.3
983 + Sama_0002 0.36 +0.1
1,019 + Sama_0002 0.40 +0.2
1,028 + Sama_0002 0.41 +0.3
1,028 + Sama_0002 0.41 +0.5
1,028 + Sama_0002 0.41 -0.3
1,029 - Sama_0002 0.41 -1.5
1,029 - Sama_0002 0.41 +0.6
1,029 - Sama_0002 0.41 -1.8
1,029 - Sama_0002 0.41 +0.3
1,062 + Sama_0002 0.44 -0.9
1,062 + Sama_0002 0.44 -0.6
1,063 - Sama_0002 0.44 +0.2
1,063 - Sama_0002 0.44 +0.3
1,115 - Sama_0002 0.50 -0.9
1,120 + Sama_0002 0.51 +0.3
1,120 + Sama_0002 0.51 -0.8
1,120 + Sama_0002 0.51 +0.6
1,120 + Sama_0002 0.51 +0.2
1,120 + Sama_0002 0.51 +0.3
1,120 + Sama_0002 0.51 -0.7
1,120 + Sama_0002 0.51 +0.6
1,164 + Sama_0002 0.55 +0.6
1,164 + Sama_0002 0.55 -0.9
1,164 + Sama_0002 0.55 +0.4
1,164 + Sama_0002 0.55 +0.6
1,165 - Sama_0002 0.56 -0.8
1,165 - Sama_0002 0.56 -1.0
1,186 + Sama_0002 0.58 -0.6
1,186 + Sama_0002 0.58 +1.0
1,186 + Sama_0002 0.58 +1.3
1,186 + Sama_0002 0.58 -0.4
1,186 + Sama_0002 0.58 -0.1
1,186 + Sama_0002 0.58 -0.0
1,187 - Sama_0002 0.58 -2.0
1,187 - Sama_0002 0.58 -0.4
1,187 - Sama_0002 0.58 +0.9
1,187 - Sama_0002 0.58 +0.2
1,187 - Sama_0002 0.58 +0.5
1,200 - Sama_0002 0.59 +0.4
1,200 - Sama_0002 0.59 +0.1
1,273 + Sama_0002 0.67 -0.5
1,273 + Sama_0002 0.67 +0.0
1,274 - Sama_0002 0.67 -0.1
1,274 - Sama_0002 0.67 -0.7
1,274 - Sama_0002 0.67 -1.1
1,313 + Sama_0002 0.72 -0.5
1,313 + Sama_0002 0.72 +0.2
1,314 - Sama_0002 0.72 -2.5
1,384 + Sama_0002 0.79 +0.5
1,384 + Sama_0002 0.79 +0.0
1,403 + Sama_0002 0.82 +0.7
1,403 + Sama_0002 0.82 +0.5
1,403 + Sama_0002 0.82 +0.1
1,403 + Sama_0002 0.82 -0.2
1,404 - Sama_0002 0.82 -0.4
1,404 - Sama_0002 0.82 +0.3
1,404 - Sama_0002 0.82 +0.2
1,404 - Sama_0002 0.82 -0.4
1,418 + Sama_0002 0.83 -0.3
1,419 - Sama_0002 0.83 -0.3
1,419 - Sama_0002 0.83 +1.3
1,419 - Sama_0002 0.83 +0.6
1,441 - Sama_0002 0.86 +0.3
1,450 + Sama_0002 0.87 -0.1
1,450 + Sama_0002 0.87 +0.9
1,450 + Sama_0002 0.87 -0.3
1,450 + Sama_0002 0.87 +1.3
1,451 - Sama_0002 0.87 -0.6
1,451 - Sama_0002 0.87 -1.0
1,451 - Sama_0002 0.87 -0.3
1,505 + +0.6
1,505 + -0.5
1,505 + +0.1
1,505 + +0.4
1,506 - -1.4

Or see this region's nucleotide sequence