Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS04870

Experiment: Lacto-N-tetraose 10 mg/mL (C)

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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 ntHMPREF1058_RS04880 and HMPREF1058_RS04875 are separated by 65 nucleotidesHMPREF1058_RS04875 and HMPREF1058_RS04870 are separated by 104 nucleotidesHMPREF1058_RS04870 and HMPREF1058_RS04865 are separated by 172 nucleotidesHMPREF1058_RS04865 and HMPREF1058_RS04860 are separated by 41 nucleotides HMPREF1058_RS04880: HMPREF1058_RS04880 - SMI1/KNR4 family protein, at 297,804 to 298,472 _RS04880 HMPREF1058_RS04875: HMPREF1058_RS04875 - hypothetical protein, at 298,538 to 299,233 _RS04875 HMPREF1058_RS04870: HMPREF1058_RS04870 - RhsIA family immunity protein, at 299,338 to 300,315 _RS04870 HMPREF1058_RS04865: HMPREF1058_RS04865 - hypothetical protein, at 300,488 to 300,955 _RS04865 HMPREF1058_RS04860: HMPREF1058_RS04860 - hypothetical protein, at 300,997 to 301,428 _RS04860 Position (kb) 299 300 301Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 298.366 kb on + strand, within HMPREF1058_RS04880at 298.376 kb on + strand, within HMPREF1058_RS04880at 298.556 kb on + strandat 298.579 kb on + strandat 298.579 kb on + strandat 298.580 kb on - strandat 298.642 kb on + strand, within HMPREF1058_RS04875at 298.643 kb on - strand, within HMPREF1058_RS04875at 298.731 kb on + strand, within HMPREF1058_RS04875at 298.732 kb on - strand, within HMPREF1058_RS04875at 298.851 kb on - strand, within HMPREF1058_RS04875at 298.911 kb on - strand, within HMPREF1058_RS04875at 298.913 kb on + strand, within HMPREF1058_RS04875at 298.914 kb on - strand, within HMPREF1058_RS04875at 298.927 kb on - strand, within HMPREF1058_RS04875at 298.998 kb on + strand, within HMPREF1058_RS04875at 299.011 kb on + strand, within HMPREF1058_RS04875at 299.016 kb on + strand, within HMPREF1058_RS04875at 299.074 kb on + strand, within HMPREF1058_RS04875at 299.079 kb on + strand, within HMPREF1058_RS04875at 299.079 kb on + strand, within HMPREF1058_RS04875at 299.080 kb on - strand, within HMPREF1058_RS04875at 299.080 kb on - strand, within HMPREF1058_RS04875at 299.080 kb on - strand, within HMPREF1058_RS04875at 299.080 kb on - strand, within HMPREF1058_RS04875at 299.100 kb on + strand, within HMPREF1058_RS04875at 299.184 kb on + strandat 299.219 kb on - strandat 299.322 kb on + strandat 299.352 kb on + strandat 299.377 kb on - strandat 299.418 kb on + strandat 299.474 kb on - strand, within HMPREF1058_RS04870at 299.562 kb on + strand, within HMPREF1058_RS04870at 299.565 kb on - strand, within HMPREF1058_RS04870at 299.606 kb on + strand, within HMPREF1058_RS04870at 299.708 kb on + strand, within HMPREF1058_RS04870at 299.807 kb on - strand, within HMPREF1058_RS04870at 299.971 kb on + strand, within HMPREF1058_RS04870at 300.073 kb on + strand, within HMPREF1058_RS04870at 300.123 kb on - strand, within HMPREF1058_RS04870at 300.197 kb on - strand, within HMPREF1058_RS04870at 300.197 kb on - strand, within HMPREF1058_RS04870at 300.372 kb on - strandat 300.389 kb on + strandat 300.389 kb on + strandat 300.420 kb on + strandat 300.420 kb on + strandat 300.475 kb on + strandat 300.550 kb on - strand, within HMPREF1058_RS04865at 300.550 kb on - strand, within HMPREF1058_RS04865at 300.595 kb on - strand, within HMPREF1058_RS04865at 300.596 kb on + strand, within HMPREF1058_RS04865at 300.596 kb on + strand, within HMPREF1058_RS04865at 300.597 kb on - strand, within HMPREF1058_RS04865at 300.597 kb on - strand, within HMPREF1058_RS04865at 300.597 kb on - strand, within HMPREF1058_RS04865at 300.633 kb on + strand, within HMPREF1058_RS04865at 300.639 kb on + strand, within HMPREF1058_RS04865at 300.639 kb on + strand, within HMPREF1058_RS04865at 300.640 kb on - strand, within HMPREF1058_RS04865at 300.640 kb on - strand, within HMPREF1058_RS04865at 300.645 kb on + strand, within HMPREF1058_RS04865at 300.646 kb on - strand, within HMPREF1058_RS04865at 300.646 kb on - strand, within HMPREF1058_RS04865at 300.646 kb on - strand, within HMPREF1058_RS04865at 300.657 kb on - strand, within HMPREF1058_RS04865at 300.657 kb on - strand, within HMPREF1058_RS04865at 300.666 kb on - strand, within HMPREF1058_RS04865at 300.672 kb on + strand, within HMPREF1058_RS04865at 300.672 kb on + strand, within HMPREF1058_RS04865at 300.673 kb on - strand, within HMPREF1058_RS04865at 300.728 kb on - strand, within HMPREF1058_RS04865at 300.749 kb on - strand, within HMPREF1058_RS04865at 300.755 kb on - strand, within HMPREF1058_RS04865at 300.771 kb on + strand, within HMPREF1058_RS04865at 300.920 kb on - strandat 300.922 kb on - strandat 300.925 kb on + strandat 300.930 kb on + strandat 300.930 kb on + strandat 300.931 kb on - strandat 300.946 kb on + strandat 300.946 kb on + strandat 300.983 kb on - strandat 300.987 kb on + strandat 301.021 kb on - strandat 301.054 kb on - strand, within HMPREF1058_RS04860at 301.071 kb on - strand, within HMPREF1058_RS04860at 301.084 kb on - strand, within HMPREF1058_RS04860at 301.198 kb on - strand, within HMPREF1058_RS04860at 301.201 kb on - strand, within HMPREF1058_RS04860at 301.204 kb on - strand, within HMPREF1058_RS04860at 301.206 kb on - strand, within HMPREF1058_RS04860at 301.206 kb on - strand, within HMPREF1058_RS04860at 301.264 kb on - strand, within HMPREF1058_RS04860at 301.269 kb on - strand, within HMPREF1058_RS04860at 301.305 kb on + strand, within HMPREF1058_RS04860

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Per-strain Table

Position Strand Gene LocusTag Fraction Lacto-N-tetraose 10 mg/mL (C)
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298,366 + HMPREF1058_RS04880 0.84 -0.4
298,376 + HMPREF1058_RS04880 0.86 +0.6
298,556 + -0.8
298,579 + -0.3
298,579 + -2.6
298,580 - -0.1
298,642 + HMPREF1058_RS04875 0.15 +2.1
298,643 - HMPREF1058_RS04875 0.15 +0.1
298,731 + HMPREF1058_RS04875 0.28 +0.6
298,732 - HMPREF1058_RS04875 0.28 +0.5
298,851 - HMPREF1058_RS04875 0.45 +1.1
298,911 - HMPREF1058_RS04875 0.54 +0.4
298,913 + HMPREF1058_RS04875 0.54 +0.6
298,914 - HMPREF1058_RS04875 0.54 -0.6
298,927 - HMPREF1058_RS04875 0.56 -1.3
298,998 + HMPREF1058_RS04875 0.66 -0.5
299,011 + HMPREF1058_RS04875 0.68 +0.3
299,016 + HMPREF1058_RS04875 0.69 +0.1
299,074 + HMPREF1058_RS04875 0.77 +0.8
299,079 + HMPREF1058_RS04875 0.78 +0.1
299,079 + HMPREF1058_RS04875 0.78 -0.8
299,080 - HMPREF1058_RS04875 0.78 -1.2
299,080 - HMPREF1058_RS04875 0.78 +1.1
299,080 - HMPREF1058_RS04875 0.78 +0.8
299,080 - HMPREF1058_RS04875 0.78 +0.6
299,100 + HMPREF1058_RS04875 0.81 +2.0
299,184 + +1.1
299,219 - -1.0
299,322 + -1.0
299,352 + -1.0
299,377 - +0.8
299,418 + +0.6
299,474 - HMPREF1058_RS04870 0.14 -0.2
299,562 + HMPREF1058_RS04870 0.23 +0.8
299,565 - HMPREF1058_RS04870 0.23 -0.3
299,606 + HMPREF1058_RS04870 0.27 -0.2
299,708 + HMPREF1058_RS04870 0.38 -0.8
299,807 - HMPREF1058_RS04870 0.48 -1.7
299,971 + HMPREF1058_RS04870 0.65 -0.7
300,073 + HMPREF1058_RS04870 0.75 +0.3
300,123 - HMPREF1058_RS04870 0.80 -0.2
300,197 - HMPREF1058_RS04870 0.88 -0.9
300,197 - HMPREF1058_RS04870 0.88 -0.3
300,372 - +1.5
300,389 + -0.2
300,389 + -1.5
300,420 + -0.7
300,420 + +0.3
300,475 + -0.3
300,550 - HMPREF1058_RS04865 0.13 -2.4
300,550 - HMPREF1058_RS04865 0.13 -1.4
300,595 - HMPREF1058_RS04865 0.23 -1.0
300,596 + HMPREF1058_RS04865 0.23 -0.2
300,596 + HMPREF1058_RS04865 0.23 +0.4
300,597 - HMPREF1058_RS04865 0.23 -1.0
300,597 - HMPREF1058_RS04865 0.23 -0.9
300,597 - HMPREF1058_RS04865 0.23 -0.7
300,633 + HMPREF1058_RS04865 0.31 -3.2
300,639 + HMPREF1058_RS04865 0.32 +0.4
300,639 + HMPREF1058_RS04865 0.32 -0.7
300,640 - HMPREF1058_RS04865 0.32 -1.0
300,640 - HMPREF1058_RS04865 0.32 +1.2
300,645 + HMPREF1058_RS04865 0.34 +0.8
300,646 - HMPREF1058_RS04865 0.34 +1.6
300,646 - HMPREF1058_RS04865 0.34 -0.9
300,646 - HMPREF1058_RS04865 0.34 +0.0
300,657 - HMPREF1058_RS04865 0.36 -0.3
300,657 - HMPREF1058_RS04865 0.36 -0.2
300,666 - HMPREF1058_RS04865 0.38 -0.5
300,672 + HMPREF1058_RS04865 0.39 +0.2
300,672 + HMPREF1058_RS04865 0.39 +2.1
300,673 - HMPREF1058_RS04865 0.40 -0.3
300,728 - HMPREF1058_RS04865 0.51 +0.2
300,749 - HMPREF1058_RS04865 0.56 +0.4
300,755 - HMPREF1058_RS04865 0.57 -0.3
300,771 + HMPREF1058_RS04865 0.60 +1.3
300,920 - +1.4
300,922 - +1.6
300,925 + +0.7
300,930 + -1.8
300,930 + -1.2
300,931 - +2.1
300,946 + -0.6
300,946 + -1.2
300,983 - -0.3
300,987 + +0.0
301,021 - +0.2
301,054 - HMPREF1058_RS04860 0.13 +2.3
301,071 - HMPREF1058_RS04860 0.17 -1.8
301,084 - HMPREF1058_RS04860 0.20 -1.8
301,198 - HMPREF1058_RS04860 0.47 +1.9
301,201 - HMPREF1058_RS04860 0.47 +2.1
301,204 - HMPREF1058_RS04860 0.48 -2.2
301,206 - HMPREF1058_RS04860 0.48 -1.5
301,206 - HMPREF1058_RS04860 0.48 -1.1
301,264 - HMPREF1058_RS04860 0.62 +0.8
301,269 - HMPREF1058_RS04860 0.63 +0.7
301,305 + HMPREF1058_RS04860 0.71 +0.8

Or see this region's nucleotide sequence