Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS16780

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day7

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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_RS16785 and HMPREF1058_RS16780 overlap by 4 nucleotidesHMPREF1058_RS16780 and HMPREF1058_RS16775 overlap by 35 nucleotidesHMPREF1058_RS16775 and HMPREF1058_RS16770 are separated by 34 nucleotides HMPREF1058_RS16785: HMPREF1058_RS16785 - putative DNA modification/repair radical SAM protein, at 598,429 to 599,697 _RS16785 HMPREF1058_RS16780: HMPREF1058_RS16780 - TIGR03915 family putative DNA repair protein, at 599,694 to 600,461 _RS16780 HMPREF1058_RS16775: HMPREF1058_RS16775 - tRNA pseudouridine(38-40) synthase TruA, at 600,427 to 601,200 _RS16775 HMPREF1058_RS16770: HMPREF1058_RS16770 - hypothetical protein, at 601,235 to 601,909 _RS16770 Position (kb) 599 600 601Strain fitness (log2 ratio) -4 -3 -2 -1 0 1at 598.740 kb on + strand, within HMPREF1058_RS16785at 598.742 kb on + strand, within HMPREF1058_RS16785at 598.830 kb on - strand, within HMPREF1058_RS16785at 598.851 kb on + strand, within HMPREF1058_RS16785at 598.852 kb on - strand, within HMPREF1058_RS16785at 598.852 kb on - strand, within HMPREF1058_RS16785at 598.852 kb on - strand, within HMPREF1058_RS16785at 598.928 kb on + strand, within HMPREF1058_RS16785at 599.027 kb on + strand, within HMPREF1058_RS16785at 599.032 kb on - strand, within HMPREF1058_RS16785at 599.143 kb on + strand, within HMPREF1058_RS16785at 599.200 kb on + strand, within HMPREF1058_RS16785at 599.202 kb on + strand, within HMPREF1058_RS16785at 599.202 kb on + strand, within HMPREF1058_RS16785at 599.210 kb on + strand, within HMPREF1058_RS16785at 599.214 kb on + strand, within HMPREF1058_RS16785at 599.219 kb on - strand, within HMPREF1058_RS16785at 599.294 kb on + strand, within HMPREF1058_RS16785at 599.311 kb on - strand, within HMPREF1058_RS16785at 599.413 kb on - strand, within HMPREF1058_RS16785at 599.414 kb on + strand, within HMPREF1058_RS16785at 599.414 kb on + strand, within HMPREF1058_RS16785at 599.515 kb on + strand, within HMPREF1058_RS16785at 599.516 kb on - strand, within HMPREF1058_RS16785at 599.537 kb on + strand, within HMPREF1058_RS16785at 599.557 kb on + strand, within HMPREF1058_RS16785at 599.558 kb on - strand, within HMPREF1058_RS16785at 599.630 kb on + strandat 599.710 kb on - strandat 599.718 kb on - strandat 599.754 kb on + strandat 599.814 kb on + strand, within HMPREF1058_RS16780at 599.833 kb on + strand, within HMPREF1058_RS16780at 599.834 kb on - strand, within HMPREF1058_RS16780at 599.834 kb on - strand, within HMPREF1058_RS16780at 599.834 kb on - strand, within HMPREF1058_RS16780at 600.070 kb on + strand, within HMPREF1058_RS16780at 600.207 kb on + strand, within HMPREF1058_RS16780at 600.208 kb on - strand, within HMPREF1058_RS16780at 600.225 kb on + strand, within HMPREF1058_RS16780at 600.234 kb on + strand, within HMPREF1058_RS16780at 600.235 kb on - strand, within HMPREF1058_RS16780at 600.238 kb on - strand, within HMPREF1058_RS16780at 600.238 kb on - strand, within HMPREF1058_RS16780at 600.239 kb on + strand, within HMPREF1058_RS16780at 600.364 kb on - strand, within HMPREF1058_RS16780at 600.419 kb on + strandat 600.420 kb on - strandat 600.442 kb on - strandat 600.487 kb on + strandat 600.528 kb on + strand, within HMPREF1058_RS16775at 600.529 kb on - strand, within HMPREF1058_RS16775at 600.624 kb on + strand, within HMPREF1058_RS16775at 600.624 kb on + strand, within HMPREF1058_RS16775at 600.625 kb on - strand, within HMPREF1058_RS16775at 600.649 kb on - strandat 600.654 kb on + strand, within HMPREF1058_RS16775at 600.654 kb on + strand, within HMPREF1058_RS16775at 600.761 kb on + strand, within HMPREF1058_RS16775at 600.809 kb on - strand, within HMPREF1058_RS16775at 600.866 kb on + strand, within HMPREF1058_RS16775at 600.869 kb on + strand, within HMPREF1058_RS16775at 600.870 kb on - strand, within HMPREF1058_RS16775at 600.874 kb on - strand, within HMPREF1058_RS16775at 600.875 kb on + strand, within HMPREF1058_RS16775at 600.944 kb on - strand, within HMPREF1058_RS16775at 600.944 kb on - strand, within HMPREF1058_RS16775at 601.069 kb on + strand, within HMPREF1058_RS16775at 601.123 kb on + strandat 601.184 kb on + strandat 601.185 kb on - strandat 601.247 kb on + strandat 601.247 kb on + strandat 601.248 kb on - strandat 601.279 kb on + strandat 601.279 kb on + strandat 601.280 kb on - strandat 601.351 kb on + strand, within HMPREF1058_RS16770at 601.363 kb on + strand, within HMPREF1058_RS16770at 601.391 kb on - strand, within HMPREF1058_RS16770

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day7
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598,740 + HMPREF1058_RS16785 0.25 +0.2
598,742 + HMPREF1058_RS16785 0.25 -1.0
598,830 - HMPREF1058_RS16785 0.32 -1.0
598,851 + HMPREF1058_RS16785 0.33 -0.4
598,852 - HMPREF1058_RS16785 0.33 -2.8
598,852 - HMPREF1058_RS16785 0.33 +0.8
598,852 - HMPREF1058_RS16785 0.33 -1.6
598,928 + HMPREF1058_RS16785 0.39 -1.3
599,027 + HMPREF1058_RS16785 0.47 -0.6
599,032 - HMPREF1058_RS16785 0.48 -0.8
599,143 + HMPREF1058_RS16785 0.56 +0.0
599,200 + HMPREF1058_RS16785 0.61 -1.6
599,202 + HMPREF1058_RS16785 0.61 -1.3
599,202 + HMPREF1058_RS16785 0.61 +1.0
599,210 + HMPREF1058_RS16785 0.62 -1.6
599,214 + HMPREF1058_RS16785 0.62 +0.2
599,219 - HMPREF1058_RS16785 0.62 -0.2
599,294 + HMPREF1058_RS16785 0.68 -0.5
599,311 - HMPREF1058_RS16785 0.70 -1.7
599,413 - HMPREF1058_RS16785 0.78 -1.1
599,414 + HMPREF1058_RS16785 0.78 -0.1
599,414 + HMPREF1058_RS16785 0.78 -2.6
599,515 + HMPREF1058_RS16785 0.86 -0.2
599,516 - HMPREF1058_RS16785 0.86 -1.6
599,537 + HMPREF1058_RS16785 0.87 -0.8
599,557 + HMPREF1058_RS16785 0.89 -0.7
599,558 - HMPREF1058_RS16785 0.89 -1.2
599,630 + -2.8
599,710 - -2.2
599,718 - +0.4
599,754 + -0.3
599,814 + HMPREF1058_RS16780 0.16 +0.9
599,833 + HMPREF1058_RS16780 0.18 -0.8
599,834 - HMPREF1058_RS16780 0.18 -1.8
599,834 - HMPREF1058_RS16780 0.18 -1.2
599,834 - HMPREF1058_RS16780 0.18 -2.1
600,070 + HMPREF1058_RS16780 0.49 -0.2
600,207 + HMPREF1058_RS16780 0.67 -1.8
600,208 - HMPREF1058_RS16780 0.67 +0.4
600,225 + HMPREF1058_RS16780 0.69 -2.4
600,234 + HMPREF1058_RS16780 0.70 +0.8
600,235 - HMPREF1058_RS16780 0.70 -1.2
600,238 - HMPREF1058_RS16780 0.71 -1.6
600,238 - HMPREF1058_RS16780 0.71 -2.0
600,239 + HMPREF1058_RS16780 0.71 +0.2
600,364 - HMPREF1058_RS16780 0.87 -2.7
600,419 + -0.2
600,420 - -0.2
600,442 - -0.5
600,487 + -2.0
600,528 + HMPREF1058_RS16775 0.13 -1.2
600,529 - HMPREF1058_RS16775 0.13 +0.8
600,624 + HMPREF1058_RS16775 0.25 -0.8
600,624 + HMPREF1058_RS16775 0.25 -2.7
600,625 - HMPREF1058_RS16775 0.26 -0.8
600,649 - -0.2
600,654 + HMPREF1058_RS16775 0.29 -2.4
600,654 + HMPREF1058_RS16775 0.29 -3.0
600,761 + HMPREF1058_RS16775 0.43 -3.1
600,809 - HMPREF1058_RS16775 0.49 -1.2
600,866 + HMPREF1058_RS16775 0.57 -2.0
600,869 + HMPREF1058_RS16775 0.57 -2.6
600,870 - HMPREF1058_RS16775 0.57 -3.8
600,874 - HMPREF1058_RS16775 0.58 -2.4
600,875 + HMPREF1058_RS16775 0.58 -1.3
600,944 - HMPREF1058_RS16775 0.67 -1.6
600,944 - HMPREF1058_RS16775 0.67 -1.2
601,069 + HMPREF1058_RS16775 0.83 -4.6
601,123 + -2.0
601,184 + -0.2
601,185 - +0.8
601,247 + -1.1
601,247 + -3.0
601,248 - -1.7
601,279 + -2.5
601,279 + -1.2
601,280 - +0.8
601,351 + HMPREF1058_RS16770 0.17 -2.7
601,363 + HMPREF1058_RS16770 0.19 -1.2
601,391 - HMPREF1058_RS16770 0.23 -3.1

Or see this region's nucleotide sequence