Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS01780

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day6

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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_RS01785 and HMPREF1058_RS01780 are separated by 198 nucleotidesHMPREF1058_RS01780 and HMPREF1058_RS01775 are separated by 33 nucleotidesHMPREF1058_RS01775 and HMPREF1058_RS01770 are separated by 190 nucleotides HMPREF1058_RS01785: HMPREF1058_RS01785 - patatin-like phospholipase family protein, at 42,352 to 44,571 _RS01785 HMPREF1058_RS01780: HMPREF1058_RS01780 - 3'-5' exonuclease, at 44,770 to 45,258 _RS01780 HMPREF1058_RS01775: HMPREF1058_RS01775 - YigZ family protein, at 45,292 to 45,894 _RS01775 HMPREF1058_RS01770: HMPREF1058_RS01770 - porin, at 46,085 to 47,098 _RS01770 Position (kb) 44 45 46Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 43.816 kb on - strand, within HMPREF1058_RS01785at 43.873 kb on + strand, within HMPREF1058_RS01785at 43.874 kb on - strand, within HMPREF1058_RS01785at 43.903 kb on + strand, within HMPREF1058_RS01785at 43.910 kb on - strand, within HMPREF1058_RS01785at 43.910 kb on - strand, within HMPREF1058_RS01785at 43.950 kb on + strand, within HMPREF1058_RS01785at 43.951 kb on - strand, within HMPREF1058_RS01785at 44.247 kb on + strand, within HMPREF1058_RS01785at 44.267 kb on - strand, within HMPREF1058_RS01785at 44.331 kb on + strand, within HMPREF1058_RS01785at 44.359 kb on - strandat 44.432 kb on - strandat 44.432 kb on - strandat 44.433 kb on + strandat 44.433 kb on + strandat 44.433 kb on + strandat 44.434 kb on - strandat 44.434 kb on - strandat 44.520 kb on + strandat 44.580 kb on - strandat 44.580 kb on - strandat 44.657 kb on + strandat 44.658 kb on - strandat 44.658 kb on - strandat 44.661 kb on + strandat 44.725 kb on - strandat 44.817 kb on + strandat 44.818 kb on - strandat 44.825 kb on + strand, within HMPREF1058_RS01780at 44.829 kb on + strand, within HMPREF1058_RS01780at 44.829 kb on + strand, within HMPREF1058_RS01780at 44.879 kb on - strand, within HMPREF1058_RS01780at 44.908 kb on + strandat 44.909 kb on - strand, within HMPREF1058_RS01780at 44.909 kb on - strand, within HMPREF1058_RS01780at 44.929 kb on - strand, within HMPREF1058_RS01780at 44.981 kb on + strand, within HMPREF1058_RS01780at 45.031 kb on - strand, within HMPREF1058_RS01780at 45.076 kb on + strand, within HMPREF1058_RS01780at 45.076 kb on + strand, within HMPREF1058_RS01780at 45.159 kb on - strand, within HMPREF1058_RS01780at 45.162 kb on + strand, within HMPREF1058_RS01780at 45.296 kb on + strandat 45.306 kb on + strandat 45.307 kb on - strandat 45.341 kb on + strandat 45.342 kb on - strandat 45.344 kb on - strandat 45.346 kb on - strandat 45.367 kb on - strand, within HMPREF1058_RS01775at 45.373 kb on - strand, within HMPREF1058_RS01775at 45.373 kb on - strand, within HMPREF1058_RS01775at 45.395 kb on + strand, within HMPREF1058_RS01775at 45.404 kb on + strand, within HMPREF1058_RS01775at 45.437 kb on - strand, within HMPREF1058_RS01775at 45.439 kb on + strand, within HMPREF1058_RS01775at 45.460 kb on + strand, within HMPREF1058_RS01775at 45.466 kb on + strand, within HMPREF1058_RS01775at 45.466 kb on + strand, within HMPREF1058_RS01775at 45.469 kb on - strand, within HMPREF1058_RS01775at 45.469 kb on - strand, within HMPREF1058_RS01775at 45.587 kb on + strand, within HMPREF1058_RS01775at 45.587 kb on + strand, within HMPREF1058_RS01775at 45.588 kb on - strand, within HMPREF1058_RS01775at 45.588 kb on - strand, within HMPREF1058_RS01775at 45.669 kb on - strand, within HMPREF1058_RS01775at 45.681 kb on + strand, within HMPREF1058_RS01775at 45.745 kb on - strand, within HMPREF1058_RS01775at 45.793 kb on + strand, within HMPREF1058_RS01775at 45.793 kb on + strand, within HMPREF1058_RS01775at 45.794 kb on - strand, within HMPREF1058_RS01775at 45.799 kb on - strand, within HMPREF1058_RS01775at 45.828 kb on + strand, within HMPREF1058_RS01775at 46.011 kb on + strandat 46.022 kb on + strandat 46.022 kb on + strandat 46.025 kb on + strandat 46.043 kb on - strandat 46.043 kb on - strandat 46.077 kb on + strandat 46.114 kb on + strandat 46.127 kb on - strandat 46.153 kb on + strandat 46.180 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day6
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43,816 - HMPREF1058_RS01785 0.66 +1.7
43,873 + HMPREF1058_RS01785 0.69 -0.7
43,874 - HMPREF1058_RS01785 0.69 -0.5
43,903 + HMPREF1058_RS01785 0.70 -1.5
43,910 - HMPREF1058_RS01785 0.70 -1.1
43,910 - HMPREF1058_RS01785 0.70 -0.2
43,950 + HMPREF1058_RS01785 0.72 +1.0
43,951 - HMPREF1058_RS01785 0.72 -1.6
44,247 + HMPREF1058_RS01785 0.85 -0.5
44,267 - HMPREF1058_RS01785 0.86 -1.5
44,331 + HMPREF1058_RS01785 0.89 -2.1
44,359 - +0.1
44,432 - -1.6
44,432 - -0.7
44,433 + +1.1
44,433 + -0.1
44,433 + -3.0
44,434 - -1.0
44,434 - -1.1
44,520 + -0.2
44,580 - +0.5
44,580 - +0.9
44,657 + -1.5
44,658 - +2.1
44,658 - -2.0
44,661 + +0.4
44,725 - -0.8
44,817 + +0.7
44,818 - -1.7
44,825 + HMPREF1058_RS01780 0.11 +0.9
44,829 + HMPREF1058_RS01780 0.12 -1.6
44,829 + HMPREF1058_RS01780 0.12 -1.7
44,879 - HMPREF1058_RS01780 0.22 +0.9
44,908 + -1.5
44,909 - HMPREF1058_RS01780 0.28 -1.7
44,909 - HMPREF1058_RS01780 0.28 -0.7
44,929 - HMPREF1058_RS01780 0.33 -0.4
44,981 + HMPREF1058_RS01780 0.43 -2.6
45,031 - HMPREF1058_RS01780 0.53 +0.3
45,076 + HMPREF1058_RS01780 0.63 +1.0
45,076 + HMPREF1058_RS01780 0.63 +0.1
45,159 - HMPREF1058_RS01780 0.80 -1.1
45,162 + HMPREF1058_RS01780 0.80 +0.3
45,296 + -0.9
45,306 + -2.1
45,307 - -0.7
45,341 + -1.7
45,342 - -0.7
45,344 - +0.4
45,346 - -1.8
45,367 - HMPREF1058_RS01775 0.12 -1.5
45,373 - HMPREF1058_RS01775 0.13 -2.4
45,373 - HMPREF1058_RS01775 0.13 -0.4
45,395 + HMPREF1058_RS01775 0.17 -1.8
45,404 + HMPREF1058_RS01775 0.19 -2.0
45,437 - HMPREF1058_RS01775 0.24 -0.9
45,439 + HMPREF1058_RS01775 0.24 -3.0
45,460 + HMPREF1058_RS01775 0.28 +1.6
45,466 + HMPREF1058_RS01775 0.29 -0.4
45,466 + HMPREF1058_RS01775 0.29 -0.7
45,469 - HMPREF1058_RS01775 0.29 -1.1
45,469 - HMPREF1058_RS01775 0.29 -0.1
45,587 + HMPREF1058_RS01775 0.49 -1.3
45,587 + HMPREF1058_RS01775 0.49 -3.0
45,588 - HMPREF1058_RS01775 0.49 -1.6
45,588 - HMPREF1058_RS01775 0.49 -1.1
45,669 - HMPREF1058_RS01775 0.63 -2.2
45,681 + HMPREF1058_RS01775 0.65 +0.1
45,745 - HMPREF1058_RS01775 0.75 -0.1
45,793 + HMPREF1058_RS01775 0.83 -0.2
45,793 + HMPREF1058_RS01775 0.83 -0.9
45,794 - HMPREF1058_RS01775 0.83 -2.5
45,799 - HMPREF1058_RS01775 0.84 -1.1
45,828 + HMPREF1058_RS01775 0.89 -0.5
46,011 + +0.1
46,022 + -0.1
46,022 + +0.2
46,025 + +0.9
46,043 - -2.3
46,043 - -1.5
46,077 + -0.0
46,114 + -1.7
46,127 - -2.0
46,153 + -2.1
46,180 - -2.1

Or see this region's nucleotide sequence