Strain Fitness in Xanthomonas campestris pv. campestris strain 8004 around Xcc-8004.477.1

Experiment: Parafilmed volatile agar plate with Trichoderma atroviridae IMI dcr2mutant

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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.

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500 ntXcc-8004.475.1 and Xcc-8004.476.1 overlap by 4 nucleotidesXcc-8004.476.1 and Xcc-8004.477.1 overlap by 4 nucleotidesXcc-8004.477.1 and Xcc-8004.478.1 are separated by 78 nucleotidesXcc-8004.478.1 and Xcc-8004.479.1 are separated by 4 nucleotides Xcc-8004.475.1: Xcc-8004.475.1 - 3-oxoadipate CoA-transferase subunit A (EC 2.8.3.6); Glutaconate CoA-transferase subunit A (EC 2.8.3.12), at 438,208 to 439,071 Xcc-8004.475.1 Xcc-8004.476.1: Xcc-8004.476.1 - 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6); Glutaconate CoA-transferase subunit B (EC 2.8.3.12), at 439,068 to 439,856 Xcc-8004.476.1 Xcc-8004.477.1: Xcc-8004.477.1 - Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-), at 439,853 to 441,061 Xcc-8004.477.1 Xcc-8004.478.1: Xcc-8004.478.1 - Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3), at 441,140 to 441,871 Xcc-8004.478.1 Xcc-8004.479.1: Xcc-8004.479.1 - Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3), at 441,876 to 442,439 Xcc-8004.479.1 Position (kb) 439 440 441 442Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 438.901 kb on + strand, within Xcc-8004.475.1at 438.901 kb on + strand, within Xcc-8004.475.1at 438.901 kb on + strand, within Xcc-8004.475.1at 438.901 kb on + strand, within Xcc-8004.475.1at 438.902 kb on - strand, within Xcc-8004.475.1at 438.902 kb on - strand, within Xcc-8004.475.1at 438.913 kb on + strand, within Xcc-8004.475.1at 438.913 kb on + strand, within Xcc-8004.475.1at 438.913 kb on + strand, within Xcc-8004.475.1at 438.914 kb on - strand, within Xcc-8004.475.1at 438.937 kb on + strand, within Xcc-8004.475.1at 438.937 kb on + strand, within Xcc-8004.475.1at 438.938 kb on - strand, within Xcc-8004.475.1at 439.039 kb on + strandat 439.039 kb on + strandat 439.039 kb on + strandat 439.040 kb on - strandat 439.215 kb on + strand, within Xcc-8004.476.1at 439.216 kb on - strand, within Xcc-8004.476.1at 439.216 kb on - strand, within Xcc-8004.476.1at 439.216 kb on - strand, within Xcc-8004.476.1at 439.216 kb on - strand, within Xcc-8004.476.1at 439.327 kb on - strand, within Xcc-8004.476.1at 439.354 kb on + strand, within Xcc-8004.476.1at 439.354 kb on + strand, within Xcc-8004.476.1at 439.354 kb on + strand, within Xcc-8004.476.1at 439.354 kb on + strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.355 kb on - strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.630 kb on + strand, within Xcc-8004.476.1at 439.631 kb on - strand, within Xcc-8004.476.1at 439.631 kb on - strand, within Xcc-8004.476.1at 439.631 kb on - strand, within Xcc-8004.476.1at 439.631 kb on - strand, within Xcc-8004.476.1at 439.865 kb on + strandat 439.866 kb on - strandat 439.866 kb on - strandat 440.009 kb on + strand, within Xcc-8004.477.1at 440.009 kb on + strand, within Xcc-8004.477.1at 440.009 kb on + strand, within Xcc-8004.477.1at 440.010 kb on - strand, within Xcc-8004.477.1at 440.010 kb on - strand, within Xcc-8004.477.1at 440.372 kb on + strand, within Xcc-8004.477.1at 440.372 kb on + strand, within Xcc-8004.477.1at 440.373 kb on - strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.735 kb on + strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 440.736 kb on - strand, within Xcc-8004.477.1at 441.016 kb on + strandat 441.036 kb on + strandat 441.036 kb on + strandat 441.222 kb on - strand, within Xcc-8004.478.1at 441.237 kb on - strand, within Xcc-8004.478.1at 441.442 kb on + strand, within Xcc-8004.478.1at 441.442 kb on + strand, within Xcc-8004.478.1at 441.442 kb on + strand, within Xcc-8004.478.1at 441.443 kb on - strand, within Xcc-8004.478.1at 441.443 kb on - strand, within Xcc-8004.478.1at 441.617 kb on + strand, within Xcc-8004.478.1at 441.617 kb on + strand, within Xcc-8004.478.1at 441.618 kb on - strand, within Xcc-8004.478.1at 441.618 kb on - strand, within Xcc-8004.478.1at 441.618 kb on - strand, within Xcc-8004.478.1at 441.618 kb on - strand, within Xcc-8004.478.1at 441.640 kb on + strand, within Xcc-8004.478.1at 441.654 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.695 kb on + strand, within Xcc-8004.478.1at 441.696 kb on - strand, within Xcc-8004.478.1at 441.696 kb on - strand, within Xcc-8004.478.1at 441.696 kb on - strand, within Xcc-8004.478.1at 441.734 kb on + strand, within Xcc-8004.478.1at 441.734 kb on + strand, within Xcc-8004.478.1at 441.734 kb on + strand, within Xcc-8004.478.1at 441.734 kb on + strand, within Xcc-8004.478.1at 441.734 kb on + strand, within Xcc-8004.478.1at 441.735 kb on - strand, within Xcc-8004.478.1at 441.735 kb on - strand, within Xcc-8004.478.1at 441.810 kb on - strandat 441.942 kb on + strand, within Xcc-8004.479.1at 441.942 kb on + strand, within Xcc-8004.479.1at 441.942 kb on + strand, within Xcc-8004.479.1at 441.942 kb on + strand, within Xcc-8004.479.1at 441.943 kb on - strand, within Xcc-8004.479.1at 441.943 kb on - strand, within Xcc-8004.479.1at 442.048 kb on + strand, within Xcc-8004.479.1at 442.048 kb on + strand, within Xcc-8004.479.1at 442.049 kb on - strand, within Xcc-8004.479.1at 442.049 kb on - strand, within Xcc-8004.479.1at 442.049 kb on - strand, within Xcc-8004.479.1at 442.049 kb on - strand, within Xcc-8004.479.1

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Per-strain Table

Position Strand Gene LocusTag Fraction Parafilmed volatile agar plate with Trichoderma atroviridae IMI dcr2mutant
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438,901 + Xcc-8004.475.1 0.80 -1.9
438,901 + Xcc-8004.475.1 0.80 -0.1
438,901 + Xcc-8004.475.1 0.80 +1.0
438,901 + Xcc-8004.475.1 0.80 -1.3
438,902 - Xcc-8004.475.1 0.80 +0.0
438,902 - Xcc-8004.475.1 0.80 -0.3
438,913 + Xcc-8004.475.1 0.82 -0.7
438,913 + Xcc-8004.475.1 0.82 -0.7
438,913 + Xcc-8004.475.1 0.82 -0.0
438,914 - Xcc-8004.475.1 0.82 -1.5
438,937 + Xcc-8004.475.1 0.84 -0.8
438,937 + Xcc-8004.475.1 0.84 -0.7
438,938 - Xcc-8004.475.1 0.84 -1.8
439,039 + -1.1
439,039 + -0.0
439,039 + -0.1
439,040 - +0.5
439,215 + Xcc-8004.476.1 0.19 -0.4
439,216 - Xcc-8004.476.1 0.19 +0.4
439,216 - Xcc-8004.476.1 0.19 -0.2
439,216 - Xcc-8004.476.1 0.19 +1.3
439,216 - Xcc-8004.476.1 0.19 +0.1
439,327 - Xcc-8004.476.1 0.33 +1.6
439,354 + Xcc-8004.476.1 0.36 -0.6
439,354 + Xcc-8004.476.1 0.36 +1.1
439,354 + Xcc-8004.476.1 0.36 -0.7
439,354 + Xcc-8004.476.1 0.36 -1.2
439,355 - Xcc-8004.476.1 0.36 -1.9
439,355 - Xcc-8004.476.1 0.36 +1.3
439,355 - Xcc-8004.476.1 0.36 +0.5
439,355 - Xcc-8004.476.1 0.36 +1.3
439,355 - Xcc-8004.476.1 0.36 +0.8
439,355 - Xcc-8004.476.1 0.36 -0.9
439,630 + Xcc-8004.476.1 0.71 -0.2
439,630 + Xcc-8004.476.1 0.71 +0.5
439,630 + Xcc-8004.476.1 0.71 -0.5
439,630 + Xcc-8004.476.1 0.71 +0.0
439,630 + Xcc-8004.476.1 0.71 +1.9
439,630 + Xcc-8004.476.1 0.71 -1.0
439,630 + Xcc-8004.476.1 0.71 +1.4
439,631 - Xcc-8004.476.1 0.71 -0.8
439,631 - Xcc-8004.476.1 0.71 -0.2
439,631 - Xcc-8004.476.1 0.71 +0.5
439,631 - Xcc-8004.476.1 0.71 -0.5
439,865 + -1.5
439,866 - -2.4
439,866 - -0.6
440,009 + Xcc-8004.477.1 0.13 -0.2
440,009 + Xcc-8004.477.1 0.13 +1.6
440,009 + Xcc-8004.477.1 0.13 +0.9
440,010 - Xcc-8004.477.1 0.13 -2.1
440,010 - Xcc-8004.477.1 0.13 +1.1
440,372 + Xcc-8004.477.1 0.43 +0.2
440,372 + Xcc-8004.477.1 0.43 +0.2
440,373 - Xcc-8004.477.1 0.43 +0.3
440,735 + Xcc-8004.477.1 0.73 -0.6
440,735 + Xcc-8004.477.1 0.73 -2.9
440,735 + Xcc-8004.477.1 0.73 +0.1
440,735 + Xcc-8004.477.1 0.73 -0.4
440,735 + Xcc-8004.477.1 0.73 +0.1
440,735 + Xcc-8004.477.1 0.73 -2.1
440,735 + Xcc-8004.477.1 0.73 +0.3
440,735 + Xcc-8004.477.1 0.73 +0.8
440,735 + Xcc-8004.477.1 0.73 +1.7
440,735 + Xcc-8004.477.1 0.73 -0.1
440,735 + Xcc-8004.477.1 0.73 -1.5
440,735 + Xcc-8004.477.1 0.73 -0.4
440,736 - Xcc-8004.477.1 0.73 +0.6
440,736 - Xcc-8004.477.1 0.73 +0.8
440,736 - Xcc-8004.477.1 0.73 -1.7
440,736 - Xcc-8004.477.1 0.73 +0.3
440,736 - Xcc-8004.477.1 0.73 -0.1
440,736 - Xcc-8004.477.1 0.73 -0.7
440,736 - Xcc-8004.477.1 0.73 +1.6
441,016 + +0.4
441,036 + +0.1
441,036 + -0.6
441,222 - Xcc-8004.478.1 0.11 +0.5
441,237 - Xcc-8004.478.1 0.13 +0.4
441,442 + Xcc-8004.478.1 0.41 +0.6
441,442 + Xcc-8004.478.1 0.41 -0.7
441,442 + Xcc-8004.478.1 0.41 -1.4
441,443 - Xcc-8004.478.1 0.41 +1.6
441,443 - Xcc-8004.478.1 0.41 +0.2
441,617 + Xcc-8004.478.1 0.65 +1.7
441,617 + Xcc-8004.478.1 0.65 +0.3
441,618 - Xcc-8004.478.1 0.65 -2.4
441,618 - Xcc-8004.478.1 0.65 -0.4
441,618 - Xcc-8004.478.1 0.65 +1.1
441,618 - Xcc-8004.478.1 0.65 -0.0
441,640 + Xcc-8004.478.1 0.68 +1.1
441,654 + Xcc-8004.478.1 0.70 +1.1
441,695 + Xcc-8004.478.1 0.76 +1.1
441,695 + Xcc-8004.478.1 0.76 +1.8
441,695 + Xcc-8004.478.1 0.76 -0.8
441,695 + Xcc-8004.478.1 0.76 -0.2
441,695 + Xcc-8004.478.1 0.76 -1.6
441,695 + Xcc-8004.478.1 0.76 +1.6
441,696 - Xcc-8004.478.1 0.76 +0.2
441,696 - Xcc-8004.478.1 0.76 +0.3
441,696 - Xcc-8004.478.1 0.76 -0.2
441,734 + Xcc-8004.478.1 0.81 +0.5
441,734 + Xcc-8004.478.1 0.81 -0.0
441,734 + Xcc-8004.478.1 0.81 +0.8
441,734 + Xcc-8004.478.1 0.81 -1.3
441,734 + Xcc-8004.478.1 0.81 -0.8
441,735 - Xcc-8004.478.1 0.81 -0.5
441,735 - Xcc-8004.478.1 0.81 +0.7
441,810 - +0.9
441,942 + Xcc-8004.479.1 0.12 -0.9
441,942 + Xcc-8004.479.1 0.12 -2.8
441,942 + Xcc-8004.479.1 0.12 +0.7
441,942 + Xcc-8004.479.1 0.12 +2.3
441,943 - Xcc-8004.479.1 0.12 -0.4
441,943 - Xcc-8004.479.1 0.12 +1.3
442,048 + Xcc-8004.479.1 0.30 +0.3
442,048 + Xcc-8004.479.1 0.30 -0.5
442,049 - Xcc-8004.479.1 0.31 -0.1
442,049 - Xcc-8004.479.1 0.31 +0.2
442,049 - Xcc-8004.479.1 0.31 -0.1
442,049 - Xcc-8004.479.1 0.31 -0.9

Or see this region's nucleotide sequence