Experiment: SMSA with Ralstonia_antibiotic_mix_minus_Polymyxin_and_CrystalViolet
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.
500 nt RPSI07_RS01610 and RPSI07_RS01615 are separated by 235 nucleotides RPSI07_RS01615 and RPSI07_RS01620 overlap by 4 nucleotides RPSI07_RS01620 and RPSI07_RS01625 are separated by 98 nucleotides RPSI07_RS01625 and RPSI07_RS24025 are separated by 254 nucleotides
RPSI07_RS01610: RPSI07_RS01610 - hypothetical protein, at 425,631 to 425,933
_RS01610
RPSI07_RS01615: RPSI07_RS01615 - hypothetical protein, at 426,169 to 426,441
_RS01615
RPSI07_RS01620: RPSI07_RS01620 - DUF2778 domain-containing protein, at 426,438 to 426,923
_RS01620
RPSI07_RS01625: RPSI07_RS01625 - hypothetical protein, at 427,022 to 427,258
_RS01625
RPSI07_RS24025: RPSI07_RS24025 - hypothetical protein, at 427,513 to 427,881
_RS24025
Position (kb) 426
427 Strain fitness (log2 ratio) -4
-3
-2
-1
0
1
2
3
4 at 425.448 kb on + strand at 425.449 kb on - strand at 425.500 kb on - strand at 425.509 kb on + strand at 425.519 kb on + strand at 425.527 kb on - strand at 425.751 kb on + strand, within RPSI07_RS01610 at 425.752 kb on - strand, within RPSI07_RS01610 at 425.790 kb on + strand, within RPSI07_RS01610 at 425.790 kb on + strand, within RPSI07_RS01610 at 425.790 kb on + strand, within RPSI07_RS01610 at 425.790 kb on + strand, within RPSI07_RS01610 at 425.791 kb on - strand, within RPSI07_RS01610 at 425.791 kb on - strand, within RPSI07_RS01610 at 425.829 kb on + strand, within RPSI07_RS01610 at 425.868 kb on - strand, within RPSI07_RS01610 at 425.868 kb on - strand, within RPSI07_RS01610 at 425.871 kb on + strand, within RPSI07_RS01610 at 425.871 kb on + strand, within RPSI07_RS01610 at 425.871 kb on + strand, within RPSI07_RS01610 at 425.871 kb on + strand, within RPSI07_RS01610 at 425.872 kb on - strand, within RPSI07_RS01610 at 425.872 kb on - strand, within RPSI07_RS01610 at 425.872 kb on - strand, within RPSI07_RS01610 at 425.872 kb on - strand, within RPSI07_RS01610 at 425.873 kb on + strand, within RPSI07_RS01610 at 425.912 kb on + strand at 426.053 kb on + strand at 426.054 kb on - strand at 426.054 kb on - strand at 426.170 kb on + strand at 426.170 kb on + strand at 426.218 kb on - strand, within RPSI07_RS01615 at 426.251 kb on + strand, within RPSI07_RS01615 at 426.251 kb on + strand, within RPSI07_RS01615 at 426.251 kb on + strand, within RPSI07_RS01615 at 426.251 kb on + strand, within RPSI07_RS01615 at 426.252 kb on - strand, within RPSI07_RS01615 at 426.252 kb on - strand, within RPSI07_RS01615 at 426.252 kb on - strand, within RPSI07_RS01615 at 426.252 kb on - strand, within RPSI07_RS01615 at 426.255 kb on + strand, within RPSI07_RS01615 at 426.255 kb on + strand, within RPSI07_RS01615 at 426.255 kb on + strand, within RPSI07_RS01615 at 426.256 kb on - strand, within RPSI07_RS01615 at 426.256 kb on - strand, within RPSI07_RS01615 at 426.256 kb on - strand, within RPSI07_RS01615 at 426.268 kb on + strand, within RPSI07_RS01615 at 426.268 kb on + strand, within RPSI07_RS01615 at 426.268 kb on + strand, within RPSI07_RS01615 at 426.269 kb on - strand, within RPSI07_RS01615 at 426.294 kb on + strand, within RPSI07_RS01615 at 426.295 kb on - strand, within RPSI07_RS01615 at 426.295 kb on - strand, within RPSI07_RS01615 at 426.351 kb on - strand, within RPSI07_RS01615 at 426.351 kb on - strand, within RPSI07_RS01615 at 426.352 kb on - strand, within RPSI07_RS01615 at 426.369 kb on - strand, within RPSI07_RS01615 at 426.369 kb on - strand, within RPSI07_RS01615 at 426.369 kb on - strand, within RPSI07_RS01615 at 426.369 kb on - strand, within RPSI07_RS01615 at 426.369 kb on - strand, within RPSI07_RS01615 at 426.401 kb on - strand, within RPSI07_RS01615 at 426.401 kb on - strand, within RPSI07_RS01615 at 426.401 kb on - strand, within RPSI07_RS01615 at 426.419 kb on + strand at 426.420 kb on - strand at 426.443 kb on + strand at 426.443 kb on + strand at 426.444 kb on - strand at 426.461 kb on - strand at 426.494 kb on + strand, within RPSI07_RS01620 at 426.494 kb on + strand, within RPSI07_RS01620 at 426.510 kb on + strand, within RPSI07_RS01620 at 426.510 kb on + strand, within RPSI07_RS01620 at 426.510 kb on + strand, within RPSI07_RS01620 at 426.511 kb on - strand, within RPSI07_RS01620 at 426.532 kb on + strand, within RPSI07_RS01620 at 426.532 kb on + strand, within RPSI07_RS01620 at 426.532 kb on + strand, within RPSI07_RS01620 at 426.533 kb on - strand, within RPSI07_RS01620 at 426.533 kb on - strand, within RPSI07_RS01620 at 426.554 kb on + strand, within RPSI07_RS01620 at 426.554 kb on + strand, within RPSI07_RS01620 at 426.554 kb on + strand, within RPSI07_RS01620 at 426.555 kb on - strand, within RPSI07_RS01620 at 426.555 kb on - strand, within RPSI07_RS01620 at 426.662 kb on - strand, within RPSI07_RS01620 at 426.678 kb on - strand, within RPSI07_RS01620 at 426.678 kb on - strand, within RPSI07_RS01620 at 426.695 kb on - strand, within RPSI07_RS01620 at 426.718 kb on + strand, within RPSI07_RS01620 at 426.718 kb on + strand, within RPSI07_RS01620 at 426.719 kb on - strand, within RPSI07_RS01620 at 426.760 kb on + strand, within RPSI07_RS01620 at 426.760 kb on + strand, within RPSI07_RS01620 at 426.760 kb on + strand, within RPSI07_RS01620 at 426.760 kb on + strand, within RPSI07_RS01620 at 426.761 kb on - strand at 426.761 kb on - strand, within RPSI07_RS01620 at 426.761 kb on - strand, within RPSI07_RS01620 at 426.761 kb on - strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.763 kb on + strand, within RPSI07_RS01620 at 426.764 kb on - strand, within RPSI07_RS01620 at 426.764 kb on - strand, within RPSI07_RS01620 at 426.764 kb on - strand, within RPSI07_RS01620 at 426.764 kb on - strand, within RPSI07_RS01620 at 426.764 kb on - strand, within RPSI07_RS01620 at 426.860 kb on + strand, within RPSI07_RS01620 at 426.861 kb on - strand, within RPSI07_RS01620 at 426.861 kb on - strand, within RPSI07_RS01620 at 426.878 kb on + strand at 426.878 kb on + strand at 426.879 kb on - strand at 426.879 kb on - strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.904 kb on + strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.905 kb on - strand at 426.909 kb on - strand at 426.956 kb on - strand at 427.039 kb on - strand at 427.039 kb on - strand at 427.039 kb on - strand at 427.047 kb on - strand, within RPSI07_RS01625 at 427.086 kb on + strand, within RPSI07_RS01625 at 427.086 kb on + strand, within RPSI07_RS01625 at 427.087 kb on - strand, within RPSI07_RS01625 at 427.087 kb on - strand, within RPSI07_RS01625 at 427.094 kb on - strand, within RPSI07_RS01625 at 427.094 kb on - strand, within RPSI07_RS01625 at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.260 kb on + strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.261 kb on - strand at 427.262 kb on - strand at 427.269 kb on + strand at 427.269 kb on + strand at 427.270 kb on - strand at 427.365 kb on + strand at 427.366 kb on - strand at 427.385 kb on + strand at 427.385 kb on + strand at 427.444 kb on + strand at 427.444 kb on + strand at 427.445 kb on - strand at 427.445 kb on - strand at 427.445 kb on - strand at 427.604 kb on + strand, within RPSI07_RS24025 at 427.604 kb on + strand, within RPSI07_RS24025 at 427.604 kb on + strand, within RPSI07_RS24025 at 427.604 kb on + strand, within RPSI07_RS24025 at 427.604 kb on + strand, within RPSI07_RS24025 at 427.605 kb on - strand, within RPSI07_RS24025 at 427.605 kb on - strand, within RPSI07_RS24025 at 427.605 kb on - strand, within RPSI07_RS24025 at 427.670 kb on - strand, within RPSI07_RS24025 at 427.719 kb on - strand, within RPSI07_RS24025 at 427.766 kb on + strand, within RPSI07_RS24025 at 427.766 kb on + strand, within RPSI07_RS24025 at 427.766 kb on + strand, within RPSI07_RS24025 at 427.766 kb on + strand, within RPSI07_RS24025 at 427.823 kb on + strand, within RPSI07_RS24025 at 427.823 kb on + strand, within RPSI07_RS24025 at 427.824 kb on - strand, within RPSI07_RS24025 at 427.824 kb on - strand, within RPSI07_RS24025 at 427.877 kb on + strand at 427.877 kb on + strand at 427.877 kb on + strand at 427.877 kb on + strand at 427.877 kb on + strand at 427.877 kb on + strand at 427.877 kb on + strand at 427.878 kb on - strand at 427.878 kb on - strand at 427.878 kb on - strand at 427.878 kb on - strand at 427.878 kb on - strand at 427.878 kb on - strand
Per-strain Table
Position Strand Gene LocusTag Fraction SMSA with Ralstonia_antibiotic_mix_minus_Polymyxin_and_CrystalViolet remove 425,448 + +1.4 425,449 - -0.2 425,500 - +2.1 425,509 + -0.9 425,519 + -0.6 425,527 - -0.9 425,751 + RPSI07_RS01610 0.40 +0.7 425,752 - RPSI07_RS01610 0.40 +0.5 425,790 + RPSI07_RS01610 0.52 +0.8 425,790 + RPSI07_RS01610 0.52 +2.0 425,790 + RPSI07_RS01610 0.52 -0.2 425,790 + RPSI07_RS01610 0.52 +0.7 425,791 - RPSI07_RS01610 0.53 -0.1 425,791 - RPSI07_RS01610 0.53 -0.4 425,829 + RPSI07_RS01610 0.65 +0.8 425,868 - RPSI07_RS01610 0.78 -0.3 425,868 - RPSI07_RS01610 0.78 -2.1 425,871 + RPSI07_RS01610 0.79 +0.4 425,871 + RPSI07_RS01610 0.79 -0.2 425,871 + RPSI07_RS01610 0.79 +0.1 425,871 + RPSI07_RS01610 0.79 +0.8 425,872 - RPSI07_RS01610 0.80 -0.5 425,872 - RPSI07_RS01610 0.80 -0.6 425,872 - RPSI07_RS01610 0.80 -2.3 425,872 - RPSI07_RS01610 0.80 -0.4 425,873 + RPSI07_RS01610 0.80 -0.6 425,912 + +0.2 426,053 + -0.8 426,054 - +0.4 426,054 - -0.7 426,170 + +2.0 426,170 + -0.3 426,218 - RPSI07_RS01615 0.18 -0.0 426,251 + RPSI07_RS01615 0.30 +0.1 426,251 + RPSI07_RS01615 0.30 -2.3 426,251 + RPSI07_RS01615 0.30 +1.2 426,251 + RPSI07_RS01615 0.30 +0.8 426,252 - RPSI07_RS01615 0.30 -0.2 426,252 - RPSI07_RS01615 0.30 +0.0 426,252 - RPSI07_RS01615 0.30 -1.2 426,252 - RPSI07_RS01615 0.30 -0.8 426,255 + RPSI07_RS01615 0.32 +1.4 426,255 + RPSI07_RS01615 0.32 +2.4 426,255 + RPSI07_RS01615 0.32 -0.9 426,256 - RPSI07_RS01615 0.32 -2.2 426,256 - RPSI07_RS01615 0.32 +1.0 426,256 - RPSI07_RS01615 0.32 -0.7 426,268 + RPSI07_RS01615 0.36 +4.1 426,268 + RPSI07_RS01615 0.36 -0.5 426,268 + RPSI07_RS01615 0.36 -0.8 426,269 - RPSI07_RS01615 0.37 -0.8 426,294 + RPSI07_RS01615 0.46 +1.2 426,295 - RPSI07_RS01615 0.46 +0.2 426,295 - RPSI07_RS01615 0.46 -0.1 426,351 - RPSI07_RS01615 0.67 +0.8 426,351 - RPSI07_RS01615 0.67 +0.4 426,352 - RPSI07_RS01615 0.67 +1.4 426,369 - RPSI07_RS01615 0.73 -0.9 426,369 - RPSI07_RS01615 0.73 +0.7 426,369 - RPSI07_RS01615 0.73 -1.1 426,369 - RPSI07_RS01615 0.73 -0.3 426,369 - RPSI07_RS01615 0.73 +2.1 426,401 - RPSI07_RS01615 0.85 -0.6 426,401 - RPSI07_RS01615 0.85 -0.5 426,401 - RPSI07_RS01615 0.85 +0.4 426,419 + -0.4 426,420 - -1.0 426,443 + -0.2 426,443 + -0.5 426,444 - -0.7 426,461 - +0.8 426,494 + RPSI07_RS01620 0.12 +0.6 426,494 + RPSI07_RS01620 0.12 -0.8 426,510 + RPSI07_RS01620 0.15 -0.4 426,510 + RPSI07_RS01620 0.15 +1.4 426,510 + RPSI07_RS01620 0.15 -0.4 426,511 - RPSI07_RS01620 0.15 +0.3 426,532 + RPSI07_RS01620 0.19 -0.6 426,532 + RPSI07_RS01620 0.19 +0.8 426,532 + RPSI07_RS01620 0.19 +0.5 426,533 - RPSI07_RS01620 0.20 +1.0 426,533 - RPSI07_RS01620 0.20 -0.2 426,554 + RPSI07_RS01620 0.24 -0.9 426,554 + RPSI07_RS01620 0.24 -2.4 426,554 + RPSI07_RS01620 0.24 -0.9 426,555 - RPSI07_RS01620 0.24 +0.9 426,555 - RPSI07_RS01620 0.24 +1.4 426,662 - RPSI07_RS01620 0.46 -0.9 426,678 - RPSI07_RS01620 0.49 -0.1 426,678 - RPSI07_RS01620 0.49 -0.1 426,695 - RPSI07_RS01620 0.53 +1.8 426,718 + RPSI07_RS01620 0.58 -0.6 426,718 + RPSI07_RS01620 0.58 -0.5 426,719 - RPSI07_RS01620 0.58 -0.9 426,760 + RPSI07_RS01620 0.66 -1.1 426,760 + RPSI07_RS01620 0.66 -1.8 426,760 + RPSI07_RS01620 0.66 -1.5 426,760 + RPSI07_RS01620 0.66 +0.3 426,761 - -3.5 426,761 - RPSI07_RS01620 0.66 -1.2 426,761 - RPSI07_RS01620 0.66 +0.6 426,761 - RPSI07_RS01620 0.66 -0.7 426,763 + RPSI07_RS01620 0.67 +0.4 426,763 + RPSI07_RS01620 0.67 +4.2 426,763 + RPSI07_RS01620 0.67 -0.6 426,763 + RPSI07_RS01620 0.67 +0.2 426,763 + RPSI07_RS01620 0.67 +0.4 426,763 + RPSI07_RS01620 0.67 -1.3 426,764 - RPSI07_RS01620 0.67 -1.7 426,764 - RPSI07_RS01620 0.67 +1.4 426,764 - RPSI07_RS01620 0.67 +0.6 426,764 - RPSI07_RS01620 0.67 +1.8 426,764 - RPSI07_RS01620 0.67 +1.4 426,860 + RPSI07_RS01620 0.87 +3.0 426,861 - RPSI07_RS01620 0.87 +1.4 426,861 - RPSI07_RS01620 0.87 -0.5 426,878 + -1.0 426,878 + +0.2 426,879 - -2.8 426,879 - -0.3 426,904 + +0.1 426,904 + -1.1 426,904 + -2.0 426,904 + -0.3 426,904 + -1.5 426,904 + -2.3 426,904 + +0.2 426,904 + +0.4 426,904 + +0.8 426,904 + -1.1 426,904 + +0.3 426,904 + -0.8 426,904 + -0.1 426,905 - -0.6 426,905 - +1.8 426,905 - +0.0 426,905 - +0.1 426,905 - -1.4 426,905 - -2.3 426,905 - -1.2 426,905 - +1.1 426,905 - -1.1 426,909 - -2.0 426,956 - -0.1 427,039 - +0.3 427,039 - +0.1 427,039 - -1.5 427,047 - RPSI07_RS01625 0.11 +1.8 427,086 + RPSI07_RS01625 0.27 -3.2 427,086 + RPSI07_RS01625 0.27 -0.3 427,087 - RPSI07_RS01625 0.27 -0.3 427,087 - RPSI07_RS01625 0.27 -1.4 427,094 - RPSI07_RS01625 0.30 -1.8 427,094 - RPSI07_RS01625 0.30 -2.1 427,260 + -0.8 427,260 + -0.4 427,260 + -1.2 427,260 + +1.4 427,260 + -1.5 427,260 + +2.0 427,260 + +0.4 427,260 + -2.2 427,260 + -1.8 427,261 - -0.8 427,261 - -1.1 427,261 - -3.0 427,261 - -0.6 427,261 - +1.0 427,261 - -0.6 427,261 - +0.4 427,261 - +3.0 427,261 - +0.2 427,261 - -1.8 427,261 - -0.0 427,261 - -1.5 427,262 - -1.0 427,269 + +4.1 427,269 + -2.6 427,270 - -0.9 427,365 + -0.2 427,366 - -1.9 427,385 + +0.6 427,385 + +0.3 427,444 + -0.1 427,444 + +2.1 427,445 - -0.0 427,445 - +0.1 427,445 - +0.4 427,604 + RPSI07_RS24025 0.25 -0.4 427,604 + RPSI07_RS24025 0.25 +0.8 427,604 + RPSI07_RS24025 0.25 -0.8 427,604 + RPSI07_RS24025 0.25 -1.5 427,604 + RPSI07_RS24025 0.25 +0.6 427,605 - RPSI07_RS24025 0.25 +2.4 427,605 - RPSI07_RS24025 0.25 -0.4 427,605 - RPSI07_RS24025 0.25 -0.7 427,670 - RPSI07_RS24025 0.43 -0.2 427,719 - RPSI07_RS24025 0.56 -2.1 427,766 + RPSI07_RS24025 0.69 +0.8 427,766 + RPSI07_RS24025 0.69 -1.4 427,766 + RPSI07_RS24025 0.69 -1.3 427,766 + RPSI07_RS24025 0.69 -1.0 427,823 + RPSI07_RS24025 0.84 -2.2 427,823 + RPSI07_RS24025 0.84 +0.2 427,824 - RPSI07_RS24025 0.84 -0.6 427,824 - RPSI07_RS24025 0.84 -3.9 427,877 + -1.6 427,877 + -0.3 427,877 + +3.6 427,877 + -0.4 427,877 + +1.2 427,877 + +0.8 427,877 + -2.6 427,878 - -0.8 427,878 - -0.0 427,878 - -0.4 427,878 - -0.6 427,878 - -0.7 427,878 - +2.3
Or see this region's nucleotide sequence