Experiment: SMSA with Ralstonia_antibiotic_mix_minus_Polymyxin_and_Chloramphenicol
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_RS03570 and RPSI07_RS03575 are separated by 163 nucleotides RPSI07_RS03575 and RPSI07_RS03580 are separated by 317 nucleotides RPSI07_RS03580 and RPSI07_RS03585 overlap by 4 nucleotides
RPSI07_RS03570: RPSI07_RS03570 - hypothetical protein, at 974,451 to 978,476
_RS03570
RPSI07_RS03575: RPSI07_RS03575 - hypothetical protein, at 978,640 to 979,017
_RS03575
RPSI07_RS03580: RPSI07_RS03580 - RNA polymerase sigma factor, at 979,335 to 979,844
_RS03580
RPSI07_RS03585: RPSI07_RS03585 - FecR family protein, at 979,841 to 980,788
_RS03585
Position (kb) 978
979
980 Strain fitness (log2 ratio) -5
-4
-3
-2
-1
0
1
2
3 at 978.072 kb on + strand, within RPSI07_RS03570 at 978.072 kb on + strand, within RPSI07_RS03570 at 978.072 kb on + strand, within RPSI07_RS03570 at 978.073 kb on - strand, within RPSI07_RS03570 at 978.073 kb on - strand, within RPSI07_RS03570 at 978.073 kb on - strand, within RPSI07_RS03570 at 978.241 kb on + strand at 978.241 kb on + strand at 978.274 kb on + strand at 978.274 kb on + strand at 978.274 kb on + strand at 978.275 kb on - strand at 978.275 kb on - strand at 978.396 kb on + strand at 978.523 kb on + strand at 978.523 kb on + strand at 978.524 kb on - strand at 978.524 kb on - strand at 978.550 kb on + strand at 978.550 kb on + strand at 978.630 kb on + strand at 978.630 kb on + strand at 978.631 kb on - strand at 978.631 kb on - strand at 978.631 kb on - strand at 978.631 kb on - strand at 978.631 kb on - strand at 978.631 kb on - strand at 978.633 kb on + strand at 978.634 kb on - strand at 978.749 kb on + strand, within RPSI07_RS03575 at 978.749 kb on + strand, within RPSI07_RS03575 at 978.749 kb on + strand, within RPSI07_RS03575 at 978.750 kb on - strand, within RPSI07_RS03575 at 978.853 kb on + strand, within RPSI07_RS03575 at 978.853 kb on + strand, within RPSI07_RS03575 at 978.853 kb on + strand, within RPSI07_RS03575 at 978.853 kb on + strand, within RPSI07_RS03575 at 978.854 kb on - strand, within RPSI07_RS03575 at 978.854 kb on - strand, within RPSI07_RS03575 at 978.881 kb on + strand, within RPSI07_RS03575 at 978.881 kb on + strand, within RPSI07_RS03575 at 978.881 kb on + strand, within RPSI07_RS03575 at 978.882 kb on - strand, within RPSI07_RS03575 at 978.906 kb on + strand, within RPSI07_RS03575 at 978.907 kb on - strand, within RPSI07_RS03575 at 978.907 kb on - strand, within RPSI07_RS03575 at 978.907 kb on - strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.908 kb on + strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 978.909 kb on - strand, within RPSI07_RS03575 at 979.071 kb on + strand at 979.071 kb on + strand at 979.071 kb on + strand at 979.071 kb on + strand at 979.129 kb on + strand at 979.129 kb on + strand at 979.129 kb on + strand at 979.129 kb on + strand at 979.130 kb on - strand at 979.130 kb on - strand at 979.130 kb on - strand at 979.234 kb on + strand at 979.234 kb on + strand at 979.234 kb on + strand at 979.234 kb on + strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.235 kb on - strand at 979.283 kb on + strand at 979.283 kb on + strand at 979.392 kb on + strand, within RPSI07_RS03580 at 979.392 kb on + strand, within RPSI07_RS03580 at 979.392 kb on + strand, within RPSI07_RS03580 at 979.392 kb on + strand, within RPSI07_RS03580 at 979.392 kb on + strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.393 kb on - strand, within RPSI07_RS03580 at 979.551 kb on + strand, within RPSI07_RS03580 at 979.551 kb on + strand, within RPSI07_RS03580 at 979.551 kb on + strand, within RPSI07_RS03580 at 979.552 kb on - strand, within RPSI07_RS03580 at 979.552 kb on - strand, within RPSI07_RS03580 at 979.552 kb on - strand, within RPSI07_RS03580 at 979.587 kb on + strand, within RPSI07_RS03580 at 979.722 kb on + strand, within RPSI07_RS03580 at 979.746 kb on + strand, within RPSI07_RS03580 at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.797 kb on + strand at 979.798 kb on - strand at 979.798 kb on - strand at 979.798 kb on - strand at 979.798 kb on - strand at 979.798 kb on - strand at 979.824 kb on + strand at 979.824 kb on + strand at 979.825 kb on - strand at 979.825 kb on - strand
Per-strain Table
Position Strand Gene LocusTag Fraction SMSA with Ralstonia_antibiotic_mix_minus_Polymyxin_and_Chloramphenicol remove 978,072 + RPSI07_RS03570 0.90 +0.4 978,072 + RPSI07_RS03570 0.90 +2.1 978,072 + RPSI07_RS03570 0.90 +0.7 978,073 - RPSI07_RS03570 0.90 -1.9 978,073 - RPSI07_RS03570 0.90 +1.5 978,073 - RPSI07_RS03570 0.90 +2.5 978,241 + +0.3 978,241 + -0.7 978,274 + +0.2 978,274 + -1.8 978,274 + -0.7 978,275 - +0.5 978,275 - -0.5 978,396 + -1.2 978,523 + -1.1 978,523 + -0.5 978,524 - -1.3 978,524 - -1.9 978,550 + -0.5 978,550 + -0.8 978,630 + -0.5 978,630 + -1.2 978,631 - -1.4 978,631 - -0.1 978,631 - -0.1 978,631 - -2.3 978,631 - -0.7 978,631 - +0.3 978,633 + +0.3 978,634 - -1.1 978,749 + RPSI07_RS03575 0.29 -0.3 978,749 + RPSI07_RS03575 0.29 +1.4 978,749 + RPSI07_RS03575 0.29 +0.4 978,750 - RPSI07_RS03575 0.29 -0.1 978,853 + RPSI07_RS03575 0.56 -1.5 978,853 + RPSI07_RS03575 0.56 -1.9 978,853 + RPSI07_RS03575 0.56 +0.6 978,853 + RPSI07_RS03575 0.56 +2.5 978,854 - RPSI07_RS03575 0.57 -0.8 978,854 - RPSI07_RS03575 0.57 -0.2 978,881 + RPSI07_RS03575 0.64 +1.3 978,881 + RPSI07_RS03575 0.64 +0.4 978,881 + RPSI07_RS03575 0.64 +1.2 978,882 - RPSI07_RS03575 0.64 -0.4 978,906 + RPSI07_RS03575 0.70 -2.7 978,907 - RPSI07_RS03575 0.71 -0.1 978,907 - RPSI07_RS03575 0.71 -1.2 978,907 - RPSI07_RS03575 0.71 -1.7 978,908 + RPSI07_RS03575 0.71 +2.0 978,908 + RPSI07_RS03575 0.71 +1.0 978,908 + RPSI07_RS03575 0.71 -0.8 978,908 + RPSI07_RS03575 0.71 +1.4 978,908 + RPSI07_RS03575 0.71 +1.3 978,908 + RPSI07_RS03575 0.71 +2.7 978,908 + RPSI07_RS03575 0.71 +0.4 978,909 - RPSI07_RS03575 0.71 -0.4 978,909 - RPSI07_RS03575 0.71 +1.4 978,909 - RPSI07_RS03575 0.71 +0.5 978,909 - RPSI07_RS03575 0.71 -0.9 978,909 - RPSI07_RS03575 0.71 +1.4 978,909 - RPSI07_RS03575 0.71 -0.9 978,909 - RPSI07_RS03575 0.71 +3.3 978,909 - RPSI07_RS03575 0.71 -0.4 979,071 + +0.1 979,071 + +0.1 979,071 + +0.5 979,071 + -0.3 979,129 + -4.9 979,129 + +0.2 979,129 + +0.1 979,129 + +2.3 979,130 - -0.4 979,130 - +0.4 979,130 - -0.5 979,234 + +0.6 979,234 + -0.2 979,234 + +0.5 979,234 + +0.8 979,235 - -0.5 979,235 - -0.4 979,235 - -1.9 979,235 - +0.0 979,235 - -0.5 979,235 - -0.6 979,235 - -3.7 979,235 - -1.8 979,283 + +0.8 979,283 + +0.5 979,392 + RPSI07_RS03580 0.11 +0.3 979,392 + RPSI07_RS03580 0.11 +0.4 979,392 + RPSI07_RS03580 0.11 -0.9 979,392 + RPSI07_RS03580 0.11 -0.4 979,392 + RPSI07_RS03580 0.11 +2.1 979,393 - RPSI07_RS03580 0.11 -1.1 979,393 - RPSI07_RS03580 0.11 +1.5 979,393 - RPSI07_RS03580 0.11 -4.7 979,393 - RPSI07_RS03580 0.11 +1.1 979,393 - RPSI07_RS03580 0.11 -2.0 979,393 - RPSI07_RS03580 0.11 +0.5 979,393 - RPSI07_RS03580 0.11 -1.5 979,393 - RPSI07_RS03580 0.11 +1.3 979,393 - RPSI07_RS03580 0.11 +0.3 979,551 + RPSI07_RS03580 0.42 +0.4 979,551 + RPSI07_RS03580 0.42 +0.2 979,551 + RPSI07_RS03580 0.42 -2.7 979,552 - RPSI07_RS03580 0.43 +0.1 979,552 - RPSI07_RS03580 0.43 -0.9 979,552 - RPSI07_RS03580 0.43 +0.5 979,587 + RPSI07_RS03580 0.49 -1.6 979,722 + RPSI07_RS03580 0.76 +0.5 979,746 + RPSI07_RS03580 0.81 -1.5 979,797 + -1.7 979,797 + +0.6 979,797 + +0.7 979,797 + -0.5 979,797 + -1.0 979,797 + +1.2 979,797 + +0.2 979,797 + +0.2 979,797 + +2.4 979,797 + -1.0 979,797 + -1.0 979,797 + -1.4 979,798 - +0.0 979,798 - -1.4 979,798 - +0.1 979,798 - +1.5 979,798 - -3.1 979,824 + +0.8 979,824 + +0.1 979,825 - +1.5 979,825 - +0.3
Or see this region's nucleotide sequence