Experiment: SMSA with Ralstonia_antibiotic_mix_minus_Chloramphenicol_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_RS09470 and RPSI07_RS09475 are separated by 8 nucleotides RPSI07_RS09475 and RPSI07_RS09480 are separated by 26 nucleotides RPSI07_RS09480 and RPSI07_RS24910 are separated by 101 nucleotides RPSI07_RS24910 and RPSI07_RS09485 are separated by 485 nucleotides
RPSI07_RS09470: RPSI07_RS09470 - ethanolamine ammonia-lyase subunit EutB, at 349,169 to 350,563
_RS09470
RPSI07_RS09475: RPSI07_RS09475 - ethanolamine ammonia-lyase subunit EutC, at 350,572 to 351,384
_RS09475
RPSI07_RS09480: RPSI07_RS09480 - exodeoxyribonuclease I, at 351,411 to 352,880
_RS09480
RPSI07_RS24910: RPSI07_RS24910 - DUF2778 domain-containing protein, at 352,982 to 353,089
_RS24910
RPSI07_RS09485: RPSI07_RS09485 - hypothetical protein, at 353,575 to 353,994
_RS09485
Position (kb) 351
352
353 Strain fitness (log2 ratio) -3
-2
-1
0
1
2
3 at 350.414 kb on + strand, within RPSI07_RS09470 at 350.414 kb on + strand, within RPSI07_RS09470 at 350.415 kb on - strand, within RPSI07_RS09470 at 350.415 kb on - strand, within RPSI07_RS09470 at 350.836 kb on + strand, within RPSI07_RS09475 at 350.836 kb on + strand, within RPSI07_RS09475 at 350.837 kb on - strand, within RPSI07_RS09475 at 350.837 kb on - strand, within RPSI07_RS09475 at 351.169 kb on + strand, within RPSI07_RS09475 at 351.169 kb on + strand, within RPSI07_RS09475 at 351.170 kb on - strand, within RPSI07_RS09475 at 351.170 kb on - strand, within RPSI07_RS09475 at 351.178 kb on + strand, within RPSI07_RS09475 at 351.178 kb on + strand, within RPSI07_RS09475 at 351.179 kb on - strand, within RPSI07_RS09475 at 351.179 kb on - strand, within RPSI07_RS09475 at 351.230 kb on + strand, within RPSI07_RS09475 at 351.231 kb on - strand, within RPSI07_RS09475 at 351.250 kb on + strand, within RPSI07_RS09475 at 351.250 kb on + strand, within RPSI07_RS09475 at 351.277 kb on + strand, within RPSI07_RS09475 at 351.278 kb on - strand, within RPSI07_RS09475 at 351.317 kb on + strand at 351.407 kb on + strand at 351.407 kb on + strand at 351.407 kb on + strand at 351.407 kb on + strand at 351.407 kb on + strand at 351.408 kb on - strand at 351.408 kb on - strand at 351.408 kb on - strand at 351.408 kb on - strand at 351.408 kb on - strand at 351.408 kb on - strand at 353.054 kb on + strand, within RPSI07_RS24910 at 353.054 kb on + strand, within RPSI07_RS24910 at 353.055 kb on - strand, within RPSI07_RS24910 at 353.055 kb on - strand, within RPSI07_RS24910 at 353.066 kb on + strand, within RPSI07_RS24910 at 353.066 kb on + strand, within RPSI07_RS24910 at 353.066 kb on + strand, within RPSI07_RS24910 at 353.066 kb on + strand, within RPSI07_RS24910 at 353.067 kb on - strand, within RPSI07_RS24910 at 353.067 kb on - strand, within RPSI07_RS24910 at 353.128 kb on + strand at 353.129 kb on - strand at 353.145 kb on + strand at 353.145 kb on + strand at 353.145 kb on + strand at 353.146 kb on - strand at 353.146 kb on - strand at 353.198 kb on + strand at 353.198 kb on + strand at 353.198 kb on + strand at 353.198 kb on + strand at 353.198 kb on + strand at 353.198 kb on + strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.199 kb on - strand at 353.339 kb on + strand at 353.339 kb on + strand at 353.339 kb on + strand at 353.339 kb on + strand at 353.339 kb on + strand at 353.340 kb on - strand at 353.340 kb on - strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.342 kb on + strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.343 kb on - strand at 353.354 kb on + strand at 353.354 kb on + strand at 353.354 kb on + strand at 353.355 kb on - strand at 353.421 kb on - strand at 353.421 kb on - strand at 353.513 kb on + strand at 353.527 kb on + strand at 353.528 kb on - strand at 353.528 kb on - strand at 353.528 kb on - strand at 353.543 kb on - strand at 353.554 kb on + strand at 353.555 kb on - strand at 353.555 kb on - strand at 353.555 kb on - strand at 353.606 kb on + strand at 353.606 kb on + strand at 353.607 kb on - strand at 353.677 kb on + strand, within RPSI07_RS09485 at 353.706 kb on - strand, within RPSI07_RS09485 at 353.706 kb on - strand, within RPSI07_RS09485 at 353.706 kb on - strand, within RPSI07_RS09485 at 353.706 kb on - strand, within RPSI07_RS09485 at 353.716 kb on + strand, within RPSI07_RS09485 at 353.717 kb on - strand, within RPSI07_RS09485 at 353.830 kb on + strand, within RPSI07_RS09485 at 353.830 kb on + strand, within RPSI07_RS09485 at 353.830 kb on + strand, within RPSI07_RS09485 at 353.845 kb on + strand, within RPSI07_RS09485 at 353.845 kb on + strand, within RPSI07_RS09485 at 353.845 kb on + strand, within RPSI07_RS09485 at 353.846 kb on - strand, within RPSI07_RS09485 at 353.846 kb on - strand, within RPSI07_RS09485 at 353.866 kb on + strand, within RPSI07_RS09485 at 353.867 kb on - strand, within RPSI07_RS09485 at 353.867 kb on - strand, within RPSI07_RS09485 at 353.867 kb on - strand, within RPSI07_RS09485
Per-strain Table
Position Strand Gene LocusTag Fraction SMSA with Ralstonia_antibiotic_mix_minus_Chloramphenicol_and_CrystalViolet remove 350,414 + RPSI07_RS09470 0.89 -1.8 350,414 + RPSI07_RS09470 0.89 +0.6 350,415 - RPSI07_RS09470 0.89 +0.4 350,415 - RPSI07_RS09470 0.89 +0.9 350,836 + RPSI07_RS09475 0.32 +1.5 350,836 + RPSI07_RS09475 0.32 +0.1 350,837 - RPSI07_RS09475 0.33 +1.4 350,837 - RPSI07_RS09475 0.33 +1.3 351,169 + RPSI07_RS09475 0.73 +0.8 351,169 + RPSI07_RS09475 0.73 +0.8 351,170 - RPSI07_RS09475 0.74 -0.6 351,170 - RPSI07_RS09475 0.74 +1.9 351,178 + RPSI07_RS09475 0.75 +0.9 351,178 + RPSI07_RS09475 0.75 -2.3 351,179 - RPSI07_RS09475 0.75 -2.0 351,179 - RPSI07_RS09475 0.75 -0.7 351,230 + RPSI07_RS09475 0.81 -0.5 351,231 - RPSI07_RS09475 0.81 -1.5 351,250 + RPSI07_RS09475 0.83 +0.0 351,250 + RPSI07_RS09475 0.83 +1.4 351,277 + RPSI07_RS09475 0.87 -2.3 351,278 - RPSI07_RS09475 0.87 -0.5 351,317 + +0.8 351,407 + +0.7 351,407 + -1.3 351,407 + -0.5 351,407 + -0.2 351,407 + -1.5 351,408 - +3.0 351,408 - -0.6 351,408 - -2.0 351,408 - +1.0 351,408 - +0.5 351,408 - -2.1 353,054 + RPSI07_RS24910 0.67 -2.0 353,054 + RPSI07_RS24910 0.67 -1.7 353,055 - RPSI07_RS24910 0.68 +2.3 353,055 - RPSI07_RS24910 0.68 +1.3 353,066 + RPSI07_RS24910 0.78 -1.1 353,066 + RPSI07_RS24910 0.78 +0.2 353,066 + RPSI07_RS24910 0.78 -0.8 353,066 + RPSI07_RS24910 0.78 -2.7 353,067 - RPSI07_RS24910 0.79 -0.5 353,067 - RPSI07_RS24910 0.79 -1.6 353,128 + -0.3 353,129 - +0.8 353,145 + +0.6 353,145 + +0.6 353,145 + +1.8 353,146 - -0.8 353,146 - -0.4 353,198 + +1.0 353,198 + -0.1 353,198 + -0.8 353,198 + +0.0 353,198 + +0.5 353,198 + -0.2 353,199 - +0.6 353,199 - -0.5 353,199 - +0.1 353,199 - -0.9 353,199 - -0.8 353,199 - +0.7 353,199 - +1.0 353,339 + -1.2 353,339 + -0.4 353,339 + +1.0 353,339 + -1.6 353,339 + +3.4 353,340 - +1.0 353,340 - -0.2 353,342 + +1.6 353,342 + +0.3 353,342 + -0.8 353,342 + -1.7 353,342 + +1.4 353,342 + -2.0 353,342 + -0.5 353,342 + +2.0 353,342 + -0.1 353,342 + +2.0 353,343 - -1.3 353,343 - +3.4 353,343 - +1.0 353,343 - -1.6 353,343 - -0.3 353,343 - -0.7 353,343 - -0.3 353,343 - -0.2 353,354 + -0.3 353,354 + -2.7 353,354 + -1.3 353,355 - +2.1 353,421 - -1.0 353,421 - -0.3 353,513 + -1.0 353,527 + +1.7 353,528 - +0.9 353,528 - -1.4 353,528 - -2.9 353,543 - +0.0 353,554 + +0.1 353,555 - +0.4 353,555 - +0.9 353,555 - -1.5 353,606 + +0.0 353,606 + +3.4 353,607 - +0.0 353,677 + RPSI07_RS09485 0.24 -1.1 353,706 - RPSI07_RS09485 0.31 +0.7 353,706 - RPSI07_RS09485 0.31 +1.0 353,706 - RPSI07_RS09485 0.31 +0.5 353,706 - RPSI07_RS09485 0.31 -0.2 353,716 + RPSI07_RS09485 0.34 -0.1 353,717 - RPSI07_RS09485 0.34 +1.3 353,830 + RPSI07_RS09485 0.61 -1.1 353,830 + RPSI07_RS09485 0.61 +0.7 353,830 + RPSI07_RS09485 0.61 +1.0 353,845 + RPSI07_RS09485 0.64 +1.0 353,845 + RPSI07_RS09485 0.64 -1.0 353,845 + RPSI07_RS09485 0.64 -0.5 353,846 - RPSI07_RS09485 0.65 +0.8 353,846 - RPSI07_RS09485 0.65 +0.8 353,866 + RPSI07_RS09485 0.69 +0.2 353,867 - RPSI07_RS09485 0.70 +2.7 353,867 - RPSI07_RS09485 0.70 -2.3 353,867 - RPSI07_RS09485 0.70 -1.8
Or see this region's nucleotide sequence