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_RS16570 and RPSI07_RS16575 are separated by 477 nucleotides RPSI07_RS16575 and RPSI07_RS16580 are separated by 776 nucleotides
RPSI07_RS16570: RPSI07_RS16570 - Type III effector protein (Skwp 4), at 1,878,939 to 1,888,208
_RS16570
RPSI07_RS16575: RPSI07_RS16575 - type III effector protein, at 1,888,686 to 1,896,041
_RS16575
RPSI07_RS16580: RPSI07_RS16580 - integrase, at 1,896,818 to 1,897,770
_RS16580
Position (kb) 1888
1889
1890
1891
1892
1893
1894
1895
1896
1897 Strain fitness (log2 ratio) -3
-2
-1
0
1
2
3
4
5
6
7
8 at 1887.761 kb on + strand at 1887.762 kb on - strand at 1887.762 kb on - strand at 1887.762 kb on - strand at 1887.821 kb on - strand at 1888.172 kb on + strand at 1888.172 kb on + strand at 1888.172 kb on + strand at 1888.172 kb on + strand at 1888.172 kb on + strand at 1888.173 kb on - strand at 1888.173 kb on - strand at 1888.209 kb on - strand at 1888.300 kb on + strand at 1888.301 kb on - strand at 1888.404 kb on + strand at 1888.405 kb on - strand at 1888.405 kb on - strand at 1888.443 kb on - strand at 1888.443 kb on - strand at 1888.443 kb on - strand at 1888.486 kb on + strand at 1888.486 kb on + strand at 1888.487 kb on - strand at 1888.514 kb on + strand at 1888.514 kb on + strand at 1888.514 kb on + strand at 1888.515 kb on - strand at 1888.515 kb on - strand at 1888.597 kb on + strand at 1888.597 kb on + strand at 1888.597 kb on + strand at 1888.598 kb on - strand at 1888.665 kb on + strand at 1888.665 kb on + strand at 1888.665 kb on + strand at 1888.666 kb on - strand at 1888.666 kb on - strand at 1888.819 kb on + strand at 1888.984 kb on + strand at 1888.985 kb on - strand at 1889.089 kb on + strand at 1889.089 kb on + strand at 1889.276 kb on - strand at 1889.615 kb on + strand, within RPSI07_RS16575 at 1889.615 kb on + strand, within RPSI07_RS16575 at 1889.615 kb on + strand, within RPSI07_RS16575 at 1889.615 kb on + strand, within RPSI07_RS16575 at 1889.616 kb on - strand, within RPSI07_RS16575 at 1889.616 kb on - strand, within RPSI07_RS16575 at 1889.616 kb on - strand, within RPSI07_RS16575 at 1889.617 kb on + strand, within RPSI07_RS16575 at 1889.617 kb on + strand, within RPSI07_RS16575 at 1889.617 kb on + strand, within RPSI07_RS16575 at 1889.618 kb on - strand, within RPSI07_RS16575 at 1889.660 kb on + strand, within RPSI07_RS16575 at 1889.818 kb on + strand, within RPSI07_RS16575 at 1889.819 kb on - strand, within RPSI07_RS16575 at 1889.819 kb on - strand, within RPSI07_RS16575 at 1889.819 kb on - strand, within RPSI07_RS16575 at 1889.847 kb on + strand, within RPSI07_RS16575 at 1889.848 kb on - strand, within RPSI07_RS16575 at 1889.848 kb on - strand, within RPSI07_RS16575 at 1889.858 kb on - strand, within RPSI07_RS16575 at 1890.265 kb on + strand, within RPSI07_RS16575 at 1890.265 kb on + strand, within RPSI07_RS16575 at 1890.266 kb on - strand, within RPSI07_RS16575 at 1890.266 kb on - strand, within RPSI07_RS16575 at 1890.334 kb on + strand, within RPSI07_RS16575 at 1890.334 kb on + strand, within RPSI07_RS16575 at 1890.433 kb on + strand, within RPSI07_RS16575 at 1890.434 kb on - strand, within RPSI07_RS16575 at 1890.573 kb on + strand, within RPSI07_RS16575 at 1890.575 kb on - strand, within RPSI07_RS16575 at 1890.799 kb on + strand, within RPSI07_RS16575 at 1890.800 kb on - strand, within RPSI07_RS16575 at 1890.800 kb on - strand, within RPSI07_RS16575 at 1890.800 kb on - strand, within RPSI07_RS16575 at 1890.800 kb on - strand, within RPSI07_RS16575 at 1890.800 kb on - strand, within RPSI07_RS16575 at 1890.847 kb on + strand, within RPSI07_RS16575 at 1890.848 kb on - strand, within RPSI07_RS16575 at 1890.848 kb on - strand, within RPSI07_RS16575 at 1890.848 kb on - strand, within RPSI07_RS16575 at 1890.992 kb on - strand, within RPSI07_RS16575 at 1891.209 kb on - strand, within RPSI07_RS16575 at 1891.444 kb on + strand, within RPSI07_RS16575 at 1891.444 kb on + strand, within RPSI07_RS16575 at 1891.445 kb on - strand, within RPSI07_RS16575 at 1891.445 kb on - strand, within RPSI07_RS16575 at 1891.445 kb on - strand, within RPSI07_RS16575 at 1891.445 kb on - strand, within RPSI07_RS16575 at 1891.450 kb on + strand, within RPSI07_RS16575 at 1891.451 kb on - strand, within RPSI07_RS16575 at 1891.621 kb on + strand, within RPSI07_RS16575 at 1891.622 kb on - strand, within RPSI07_RS16575 at 1891.622 kb on - strand, within RPSI07_RS16575 at 1891.622 kb on - strand, within RPSI07_RS16575 at 1891.645 kb on - strand, within RPSI07_RS16575 at 1891.693 kb on + strand, within RPSI07_RS16575 at 1891.693 kb on + strand, within RPSI07_RS16575 at 1891.762 kb on + strand, within RPSI07_RS16575 at 1891.762 kb on + strand, within RPSI07_RS16575 at 1891.762 kb on + strand, within RPSI07_RS16575 at 1891.762 kb on + strand, within RPSI07_RS16575 at 1891.763 kb on - strand, within RPSI07_RS16575 at 1891.763 kb on - strand, within RPSI07_RS16575 at 1891.763 kb on - strand, within RPSI07_RS16575 at 1891.763 kb on - strand, within RPSI07_RS16575 at 1891.763 kb on - strand, within RPSI07_RS16575 at 1891.819 kb on + strand, within RPSI07_RS16575 at 1892.205 kb on + strand, within RPSI07_RS16575 at 1892.205 kb on + strand, within RPSI07_RS16575 at 1892.205 kb on + strand, within RPSI07_RS16575 at 1892.205 kb on + strand, within RPSI07_RS16575 at 1892.206 kb on - strand, within RPSI07_RS16575 at 1892.428 kb on + strand, within RPSI07_RS16575 at 1892.428 kb on + strand, within RPSI07_RS16575 at 1892.428 kb on + strand, within RPSI07_RS16575 at 1892.428 kb on + strand, within RPSI07_RS16575 at 1892.428 kb on + strand, within RPSI07_RS16575 at 1892.429 kb on - strand, within RPSI07_RS16575 at 1892.831 kb on - strand, within RPSI07_RS16575 at 1892.831 kb on - strand, within RPSI07_RS16575 at 1892.944 kb on + strand, within RPSI07_RS16575 at 1894.450 kb on + strand, within RPSI07_RS16575 at 1895.047 kb on - strand at 1895.047 kb on - strand, within RPSI07_RS16575 at 1895.047 kb on - strand, within RPSI07_RS16575 at 1895.412 kb on - strand at 1895.560 kb on + strand at 1895.560 kb on + strand at 1895.560 kb on + strand at 1895.561 kb on - strand at 1895.561 kb on - strand at 1895.561 kb on - strand at 1895.561 kb on - strand at 1895.647 kb on + strand at 1895.647 kb on + strand at 1895.647 kb on + strand at 1895.648 kb on - strand at 1895.648 kb on - strand at 1895.648 kb on - strand at 1895.882 kb on - strand at 1895.918 kb on - strand at 1895.918 kb on - strand at 1896.123 kb on + strand at 1896.124 kb on - strand at 1896.140 kb on + strand at 1896.140 kb on + strand at 1896.141 kb on - strand at 1896.141 kb on - strand at 1896.141 kb on - strand at 1896.141 kb on - strand at 1896.389 kb on - strand at 1896.389 kb on - strand at 1896.389 kb on - strand at 1896.392 kb on - strand at 1896.455 kb on + strand at 1896.455 kb on + strand at 1896.456 kb on - strand at 1896.461 kb on + strand at 1896.462 kb on - strand at 1896.901 kb on + strand at 1896.935 kb on + strand, within RPSI07_RS16580 at 1896.990 kb on + strand, within RPSI07_RS16580 at 1896.991 kb on - strand, within RPSI07_RS16580 at 1896.998 kb on + strand, within RPSI07_RS16580 at 1897.010 kb on + strand, within RPSI07_RS16580 at 1897.011 kb on - strand, within RPSI07_RS16580 at 1897.011 kb on - strand, within RPSI07_RS16580 at 1897.020 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.022 kb on + strand, within RPSI07_RS16580 at 1897.023 kb on - strand, within RPSI07_RS16580 at 1897.023 kb on - strand, within RPSI07_RS16580 at 1897.023 kb on - strand, within RPSI07_RS16580 at 1897.041 kb on + strand, within RPSI07_RS16580 at 1897.041 kb on + strand, within RPSI07_RS16580
Per-strain Table
Position Strand Gene LocusTag Fraction SMSA with Ralstonia_antibiotic_mix_minus_Chloramphenicol_and_CrystalViolet remove 1,887,761 + -0.0 1,887,762 - +1.2 1,887,762 - +1.3 1,887,762 - +1.5 1,887,821 - +0.6 1,888,172 + +1.4 1,888,172 + +1.0 1,888,172 + +0.1 1,888,172 + +2.6 1,888,172 + +2.0 1,888,173 - -1.0 1,888,173 - -0.1 1,888,209 - +3.2 1,888,300 + -0.5 1,888,301 - -1.4 1,888,404 + -1.3 1,888,405 - -0.5 1,888,405 - -0.0 1,888,443 - +0.9 1,888,443 - +0.0 1,888,443 - +1.0 1,888,486 + -0.4 1,888,486 + +0.0 1,888,487 - -0.7 1,888,514 + -1.5 1,888,514 + -0.0 1,888,514 + -1.4 1,888,515 - -0.4 1,888,515 - +1.0 1,888,597 + -0.8 1,888,597 + -1.7 1,888,597 + -1.8 1,888,598 - -0.2 1,888,665 + +2.6 1,888,665 + -0.5 1,888,665 + -1.5 1,888,666 - -0.5 1,888,666 - +0.3 1,888,819 + +0.3 1,888,984 + +0.0 1,888,985 - -0.2 1,889,089 + -1.1 1,889,089 + +0.5 1,889,276 - +0.8 1,889,615 + RPSI07_RS16575 0.13 -0.5 1,889,615 + RPSI07_RS16575 0.13 +1.0 1,889,615 + RPSI07_RS16575 0.13 -0.2 1,889,615 + RPSI07_RS16575 0.13 -0.0 1,889,616 - RPSI07_RS16575 0.13 -0.1 1,889,616 - RPSI07_RS16575 0.13 +1.0 1,889,616 - RPSI07_RS16575 0.13 +0.2 1,889,617 + RPSI07_RS16575 0.13 +0.4 1,889,617 + RPSI07_RS16575 0.13 -0.5 1,889,617 + RPSI07_RS16575 0.13 +0.3 1,889,618 - RPSI07_RS16575 0.13 +0.0 1,889,660 + RPSI07_RS16575 0.13 +1.0 1,889,818 + RPSI07_RS16575 0.15 +0.5 1,889,819 - RPSI07_RS16575 0.15 -1.8 1,889,819 - RPSI07_RS16575 0.15 -0.9 1,889,819 - RPSI07_RS16575 0.15 +0.5 1,889,847 + RPSI07_RS16575 0.16 +0.9 1,889,848 - RPSI07_RS16575 0.16 +0.2 1,889,848 - RPSI07_RS16575 0.16 -1.3 1,889,858 - RPSI07_RS16575 0.16 -0.2 1,890,265 + RPSI07_RS16575 0.21 +0.6 1,890,265 + RPSI07_RS16575 0.21 +0.4 1,890,266 - RPSI07_RS16575 0.21 +0.9 1,890,266 - RPSI07_RS16575 0.21 -1.5 1,890,334 + RPSI07_RS16575 0.22 -1.8 1,890,334 + RPSI07_RS16575 0.22 +0.0 1,890,433 + RPSI07_RS16575 0.24 +0.0 1,890,434 - RPSI07_RS16575 0.24 -1.3 1,890,573 + RPSI07_RS16575 0.26 -0.6 1,890,575 - RPSI07_RS16575 0.26 +0.0 1,890,799 + RPSI07_RS16575 0.29 -0.5 1,890,800 - RPSI07_RS16575 0.29 -0.0 1,890,800 - RPSI07_RS16575 0.29 +0.3 1,890,800 - RPSI07_RS16575 0.29 -1.8 1,890,800 - RPSI07_RS16575 0.29 -0.3 1,890,800 - RPSI07_RS16575 0.29 +3.1 1,890,847 + RPSI07_RS16575 0.29 +2.6 1,890,848 - RPSI07_RS16575 0.29 -0.1 1,890,848 - RPSI07_RS16575 0.29 +0.7 1,890,848 - RPSI07_RS16575 0.29 -1.0 1,890,992 - RPSI07_RS16575 0.31 -2.0 1,891,209 - RPSI07_RS16575 0.34 -1.0 1,891,444 + RPSI07_RS16575 0.37 +0.5 1,891,444 + RPSI07_RS16575 0.37 -0.6 1,891,445 - RPSI07_RS16575 0.38 -1.0 1,891,445 - RPSI07_RS16575 0.38 -1.8 1,891,445 - RPSI07_RS16575 0.38 -0.3 1,891,445 - RPSI07_RS16575 0.38 +0.2 1,891,450 + RPSI07_RS16575 0.38 +0.4 1,891,451 - RPSI07_RS16575 0.38 -0.3 1,891,621 + RPSI07_RS16575 0.40 +1.0 1,891,622 - RPSI07_RS16575 0.40 -1.9 1,891,622 - RPSI07_RS16575 0.40 +2.6 1,891,622 - RPSI07_RS16575 0.40 +0.8 1,891,645 - RPSI07_RS16575 0.40 -0.3 1,891,693 + RPSI07_RS16575 0.41 -0.4 1,891,693 + RPSI07_RS16575 0.41 -0.6 1,891,762 + RPSI07_RS16575 0.42 -1.0 1,891,762 + RPSI07_RS16575 0.42 +1.0 1,891,762 + RPSI07_RS16575 0.42 -0.3 1,891,762 + RPSI07_RS16575 0.42 +1.2 1,891,763 - RPSI07_RS16575 0.42 +0.5 1,891,763 - RPSI07_RS16575 0.42 -0.8 1,891,763 - RPSI07_RS16575 0.42 -2.3 1,891,763 - RPSI07_RS16575 0.42 +0.6 1,891,763 - RPSI07_RS16575 0.42 +0.2 1,891,819 + RPSI07_RS16575 0.43 -0.1 1,892,205 + RPSI07_RS16575 0.48 -1.3 1,892,205 + RPSI07_RS16575 0.48 +0.2 1,892,205 + RPSI07_RS16575 0.48 -2.2 1,892,205 + RPSI07_RS16575 0.48 -1.5 1,892,206 - RPSI07_RS16575 0.48 -0.0 1,892,428 + RPSI07_RS16575 0.51 -1.2 1,892,428 + RPSI07_RS16575 0.51 +0.5 1,892,428 + RPSI07_RS16575 0.51 -0.0 1,892,428 + RPSI07_RS16575 0.51 -0.9 1,892,428 + RPSI07_RS16575 0.51 +0.5 1,892,429 - RPSI07_RS16575 0.51 -1.4 1,892,831 - RPSI07_RS16575 0.56 -0.5 1,892,831 - RPSI07_RS16575 0.56 -2.8 1,892,944 + RPSI07_RS16575 0.58 -0.9 1,894,450 + RPSI07_RS16575 0.78 -1.9 1,895,047 - -2.1 1,895,047 - RPSI07_RS16575 0.86 +0.2 1,895,047 - RPSI07_RS16575 0.86 -2.4 1,895,412 - -1.1 1,895,560 + -0.7 1,895,560 + +1.5 1,895,560 + -2.2 1,895,561 - -0.5 1,895,561 - -0.2 1,895,561 - -0.8 1,895,561 - -0.1 1,895,647 + +0.2 1,895,647 + +0.2 1,895,647 + -1.0 1,895,648 - -0.4 1,895,648 - -0.1 1,895,648 - +0.5 1,895,882 - +0.4 1,895,918 - +0.6 1,895,918 - -0.5 1,896,123 + +2.0 1,896,124 - +0.2 1,896,140 + -2.0 1,896,140 + -0.0 1,896,141 - +0.6 1,896,141 - -0.5 1,896,141 - +0.2 1,896,141 - +7.9 1,896,389 - -0.4 1,896,389 - +1.0 1,896,389 - -2.3 1,896,392 - -0.0 1,896,455 + +0.0 1,896,455 + -0.5 1,896,456 - -1.2 1,896,461 + +0.4 1,896,462 - +3.7 1,896,901 + +0.0 1,896,935 + RPSI07_RS16580 0.12 +2.0 1,896,990 + RPSI07_RS16580 0.18 +0.2 1,896,991 - RPSI07_RS16580 0.18 -1.0 1,896,998 + RPSI07_RS16580 0.19 -1.5 1,897,010 + RPSI07_RS16580 0.20 +1.1 1,897,011 - RPSI07_RS16580 0.20 -1.4 1,897,011 - RPSI07_RS16580 0.20 -0.8 1,897,020 + RPSI07_RS16580 0.21 +0.0 1,897,022 + RPSI07_RS16580 0.21 -0.4 1,897,022 + RPSI07_RS16580 0.21 -0.9 1,897,022 + RPSI07_RS16580 0.21 +0.0 1,897,022 + RPSI07_RS16580 0.21 +0.3 1,897,022 + RPSI07_RS16580 0.21 -0.2 1,897,022 + RPSI07_RS16580 0.21 +0.6 1,897,023 - RPSI07_RS16580 0.22 -0.5 1,897,023 - RPSI07_RS16580 0.22 -0.2 1,897,023 - RPSI07_RS16580 0.22 +1.0 1,897,041 + RPSI07_RS16580 0.23 -1.1 1,897,041 + RPSI07_RS16580 0.23 +0.6
Or see this region's nucleotide sequence