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_RS12315 and RPSI07_RS12320 are separated by 64 nucleotides RPSI07_RS12320 and RPSI07_RS12325 are separated by 181 nucleotides RPSI07_RS12325 and RPSI07_RS12330 are separated by 95 nucleotides RPSI07_RS12330 and RPSI07_RS12335 are separated by 18 nucleotides
RPSI07_RS12315: RPSI07_RS12315 - arogenate dehydratase, at 958,761 to 959,564
_RS12315
RPSI07_RS12320: RPSI07_RS12320 - hypothetical protein, at 959,629 to 960,021
_RS12320
RPSI07_RS12325: RPSI07_RS12325 - signal peptidase, at 960,203 to 961,219
_RS12325
RPSI07_RS12330: RPSI07_RS12330 - hypothetical protein, at 961,315 to 961,587
_RS12330
RPSI07_RS12335: RPSI07_RS12335 - type II toxin-antitoxin system HipA family toxin, at 961,606 to 962,931
_RS12335
Position (kb) 960
961
962 Strain fitness (log2 ratio) -2
-1
0
1
2
3
4
5
6
7 at 959.218 kb on + strand, within RPSI07_RS12315 at 959.218 kb on + strand, within RPSI07_RS12315 at 959.218 kb on + strand, within RPSI07_RS12315 at 959.218 kb on + strand, within RPSI07_RS12315 at 959.219 kb on - strand, within RPSI07_RS12315 at 959.219 kb on - strand, within RPSI07_RS12315 at 959.413 kb on + strand, within RPSI07_RS12315 at 959.413 kb on + strand, within RPSI07_RS12315 at 959.414 kb on - strand, within RPSI07_RS12315 at 959.428 kb on + strand, within RPSI07_RS12315 at 959.428 kb on + strand, within RPSI07_RS12315 at 959.564 kb on + strand at 959.564 kb on + strand at 959.564 kb on + strand at 959.565 kb on - strand at 959.565 kb on - strand at 959.565 kb on - strand at 959.565 kb on - strand at 959.630 kb on + strand at 959.630 kb on + strand at 959.631 kb on - strand at 959.631 kb on - strand at 959.816 kb on + strand, within RPSI07_RS12320 at 959.816 kb on + strand, within RPSI07_RS12320 at 959.816 kb on + strand, within RPSI07_RS12320 at 959.817 kb on - strand, within RPSI07_RS12320 at 959.817 kb on - strand, within RPSI07_RS12320 at 959.908 kb on + strand, within RPSI07_RS12320 at 959.908 kb on + strand, within RPSI07_RS12320 at 959.909 kb on - strand at 959.909 kb on - strand, within RPSI07_RS12320 at 959.917 kb on - strand, within RPSI07_RS12320 at 960.056 kb on - strand at 960.126 kb on - strand at 960.187 kb on - strand at 960.187 kb on - strand at 960.323 kb on + strand, within RPSI07_RS12325 at 960.324 kb on - strand, within RPSI07_RS12325 at 960.416 kb on + strand, within RPSI07_RS12325 at 960.416 kb on + strand, within RPSI07_RS12325 at 960.417 kb on - strand, within RPSI07_RS12325 at 960.417 kb on - strand, within RPSI07_RS12325 at 960.417 kb on - strand, within RPSI07_RS12325 at 960.417 kb on - strand, within RPSI07_RS12325 at 960.605 kb on + strand, within RPSI07_RS12325 at 960.605 kb on + strand, within RPSI07_RS12325 at 960.606 kb on - strand, within RPSI07_RS12325 at 960.606 kb on - strand, within RPSI07_RS12325 at 960.606 kb on - strand, within RPSI07_RS12325 at 960.606 kb on - strand, within RPSI07_RS12325 at 960.643 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.644 kb on + strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.645 kb on - strand, within RPSI07_RS12325 at 960.732 kb on - strand, within RPSI07_RS12325 at 960.732 kb on - strand, within RPSI07_RS12325 at 960.826 kb on + strand, within RPSI07_RS12325 at 960.826 kb on + strand, within RPSI07_RS12325 at 960.827 kb on - strand, within RPSI07_RS12325 at 960.827 kb on - strand, within RPSI07_RS12325 at 960.909 kb on - strand, within RPSI07_RS12325 at 960.950 kb on + strand, within RPSI07_RS12325 at 960.951 kb on - strand, within RPSI07_RS12325 at 960.951 kb on - strand, within RPSI07_RS12325 at 961.272 kb on + strand at 961.272 kb on + strand at 961.273 kb on - strand at 961.273 kb on - strand at 961.394 kb on + strand, within RPSI07_RS12330 at 961.450 kb on + strand, within RPSI07_RS12330 at 961.530 kb on + strand, within RPSI07_RS12330 at 961.530 kb on + strand, within RPSI07_RS12330 at 961.530 kb on + strand, within RPSI07_RS12330 at 961.530 kb on + strand, within RPSI07_RS12330 at 961.585 kb on + strand at 961.586 kb on - strand at 961.586 kb on - strand at 961.806 kb on - strand, within RPSI07_RS12335 at 961.806 kb on - strand, within RPSI07_RS12335 at 961.856 kb on + strand, within RPSI07_RS12335 at 961.857 kb on - strand, within RPSI07_RS12335 at 961.857 kb on - strand, within RPSI07_RS12335 at 961.928 kb on + strand, within RPSI07_RS12335 at 961.928 kb on + strand, within RPSI07_RS12335 at 961.928 kb on + strand, within RPSI07_RS12335 at 962.138 kb on + strand, within RPSI07_RS12335 at 962.138 kb on + strand, within RPSI07_RS12335 at 962.139 kb on - strand, within RPSI07_RS12335 at 962.139 kb on - strand, within RPSI07_RS12335 at 962.180 kb on + strand, within RPSI07_RS12335 at 962.181 kb on - strand, within RPSI07_RS12335 at 962.181 kb on - strand, within RPSI07_RS12335
Per-strain Table
Position Strand Gene LocusTag Fraction SMSA with Ralstonia_antibiotic_mix_minus_Polymyxin_and_CrystalViolet remove 959,218 + RPSI07_RS12315 0.57 -0.6 959,218 + RPSI07_RS12315 0.57 -0.9 959,218 + RPSI07_RS12315 0.57 -0.3 959,218 + RPSI07_RS12315 0.57 +1.1 959,219 - RPSI07_RS12315 0.57 +0.6 959,219 - RPSI07_RS12315 0.57 -2.3 959,413 + RPSI07_RS12315 0.81 +0.5 959,413 + RPSI07_RS12315 0.81 -1.2 959,414 - RPSI07_RS12315 0.81 +2.0 959,428 + RPSI07_RS12315 0.83 +0.4 959,428 + RPSI07_RS12315 0.83 +0.1 959,564 + +1.3 959,564 + -0.0 959,564 + -0.9 959,565 - +1.4 959,565 - +0.1 959,565 - -0.4 959,565 - -1.0 959,630 + +1.4 959,630 + -0.2 959,631 - -0.2 959,631 - -0.5 959,816 + RPSI07_RS12320 0.48 +1.1 959,816 + RPSI07_RS12320 0.48 +2.4 959,816 + RPSI07_RS12320 0.48 +1.3 959,817 - RPSI07_RS12320 0.48 -0.4 959,817 - RPSI07_RS12320 0.48 -1.3 959,908 + RPSI07_RS12320 0.71 +1.8 959,908 + RPSI07_RS12320 0.71 +3.7 959,909 - +1.4 959,909 - RPSI07_RS12320 0.71 +1.5 959,917 - RPSI07_RS12320 0.73 -0.3 960,056 - -1.3 960,126 - -0.2 960,187 - +0.4 960,187 - -2.3 960,323 + RPSI07_RS12325 0.12 -0.9 960,324 - RPSI07_RS12325 0.12 -0.2 960,416 + RPSI07_RS12325 0.21 +1.4 960,416 + RPSI07_RS12325 0.21 +0.4 960,417 - RPSI07_RS12325 0.21 -0.9 960,417 - RPSI07_RS12325 0.21 +1.1 960,417 - RPSI07_RS12325 0.21 -0.8 960,417 - RPSI07_RS12325 0.21 -0.7 960,605 + RPSI07_RS12325 0.40 -0.9 960,605 + RPSI07_RS12325 0.40 +3.0 960,606 - RPSI07_RS12325 0.40 +1.4 960,606 - RPSI07_RS12325 0.40 +1.4 960,606 - RPSI07_RS12325 0.40 +2.3 960,606 - RPSI07_RS12325 0.40 -0.0 960,643 + RPSI07_RS12325 0.43 -0.9 960,644 + RPSI07_RS12325 0.43 -0.8 960,644 + RPSI07_RS12325 0.43 +1.4 960,644 + RPSI07_RS12325 0.43 -1.4 960,644 + RPSI07_RS12325 0.43 -0.5 960,644 + RPSI07_RS12325 0.43 -1.6 960,644 + RPSI07_RS12325 0.43 -2.1 960,645 - RPSI07_RS12325 0.43 +0.4 960,645 - RPSI07_RS12325 0.43 +0.6 960,645 - RPSI07_RS12325 0.43 -1.2 960,645 - RPSI07_RS12325 0.43 -1.7 960,645 - RPSI07_RS12325 0.43 -1.9 960,645 - RPSI07_RS12325 0.43 +0.2 960,645 - RPSI07_RS12325 0.43 -1.5 960,645 - RPSI07_RS12325 0.43 +0.6 960,645 - RPSI07_RS12325 0.43 +0.2 960,732 - RPSI07_RS12325 0.52 +0.8 960,732 - RPSI07_RS12325 0.52 +0.5 960,826 + RPSI07_RS12325 0.61 +0.5 960,826 + RPSI07_RS12325 0.61 -0.3 960,827 - RPSI07_RS12325 0.61 -0.2 960,827 - RPSI07_RS12325 0.61 -1.2 960,909 - RPSI07_RS12325 0.69 -0.1 960,950 + RPSI07_RS12325 0.73 +0.1 960,951 - RPSI07_RS12325 0.74 +2.2 960,951 - RPSI07_RS12325 0.74 -0.0 961,272 + -0.6 961,272 + -0.3 961,273 - -1.6 961,273 - +0.3 961,394 + RPSI07_RS12330 0.29 -0.6 961,450 + RPSI07_RS12330 0.49 +0.3 961,530 + RPSI07_RS12330 0.79 -1.1 961,530 + RPSI07_RS12330 0.79 +0.8 961,530 + RPSI07_RS12330 0.79 -0.2 961,530 + RPSI07_RS12330 0.79 -1.4 961,585 + -0.9 961,586 - +1.4 961,586 - +2.7 961,806 - RPSI07_RS12335 0.15 +2.0 961,806 - RPSI07_RS12335 0.15 +0.4 961,856 + RPSI07_RS12335 0.19 +1.4 961,857 - RPSI07_RS12335 0.19 +1.9 961,857 - RPSI07_RS12335 0.19 +2.1 961,928 + RPSI07_RS12335 0.24 +2.0 961,928 + RPSI07_RS12335 0.24 +1.6 961,928 + RPSI07_RS12335 0.24 +2.2 962,138 + RPSI07_RS12335 0.40 -0.3 962,138 + RPSI07_RS12335 0.40 +1.7 962,139 - RPSI07_RS12335 0.40 +1.1 962,139 - RPSI07_RS12335 0.40 +2.4 962,180 + RPSI07_RS12335 0.43 +6.8 962,181 - RPSI07_RS12335 0.43 +2.1 962,181 - RPSI07_RS12335 0.43 +3.5
Or see this region's nucleotide sequence