Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS14340

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day4

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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_RS14345 and HMPREF1058_RS14340 are separated by 21 nucleotidesHMPREF1058_RS14340 and HMPREF1058_RS0119435 are separated by 595 nucleotides HMPREF1058_RS14345: HMPREF1058_RS14345 - RagB/SusD family nutrient uptake outer membrane protein, at 1,224,306 to 1,226,363 _RS14345 HMPREF1058_RS14340: HMPREF1058_RS14340 - TonB-dependent receptor, at 1,226,385 to 1,229,609 _RS14340 HMPREF1058_RS0119435: HMPREF1058_RS0119435 - IS982 family transposase, at 1,230,205 to 1,230,984 _RS0119435 Position (kb) 1226 1227 1228 1229 1230Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3 4at 1225.493 kb on + strand, within HMPREF1058_RS14345at 1225.494 kb on - strand, within HMPREF1058_RS14345at 1225.577 kb on + strand, within HMPREF1058_RS14345at 1225.580 kb on - strand, within HMPREF1058_RS14345at 1225.580 kb on - strand, within HMPREF1058_RS14345at 1225.640 kb on - strand, within HMPREF1058_RS14345at 1225.705 kb on - strand, within HMPREF1058_RS14345at 1225.735 kb on + strand, within HMPREF1058_RS14345at 1225.736 kb on - strand, within HMPREF1058_RS14345at 1225.821 kb on + strand, within HMPREF1058_RS14345at 1225.833 kb on - strand, within HMPREF1058_RS14345at 1225.892 kb on - strand, within HMPREF1058_RS14345at 1225.927 kb on + strand, within HMPREF1058_RS14345at 1225.927 kb on + strand, within HMPREF1058_RS14345at 1225.928 kb on - strand, within HMPREF1058_RS14345at 1226.014 kb on - strand, within HMPREF1058_RS14345at 1226.014 kb on - strand, within HMPREF1058_RS14345at 1226.101 kb on - strand, within HMPREF1058_RS14345at 1226.108 kb on + strand, within HMPREF1058_RS14345at 1226.109 kb on - strand, within HMPREF1058_RS14345at 1226.188 kb on - strandat 1226.197 kb on + strandat 1226.200 kb on + strandat 1226.201 kb on - strandat 1226.201 kb on - strandat 1226.204 kb on + strandat 1226.204 kb on + strandat 1226.220 kb on + strandat 1226.534 kb on - strandat 1226.618 kb on - strandat 1226.635 kb on + strandat 1226.636 kb on - strandat 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.077 kb on + strand, within HMPREF1058_RS14340at 1227.078 kb on - strand, within HMPREF1058_RS14340at 1227.078 kb on - strand, within HMPREF1058_RS14340at 1227.079 kb on + strand, within HMPREF1058_RS14340at 1227.112 kb on + strand, within HMPREF1058_RS14340at 1227.112 kb on + strand, within HMPREF1058_RS14340at 1227.113 kb on - strand, within HMPREF1058_RS14340at 1227.170 kb on + strand, within HMPREF1058_RS14340at 1227.205 kb on + strand, within HMPREF1058_RS14340at 1227.261 kb on - strand, within HMPREF1058_RS14340at 1227.336 kb on - strand, within HMPREF1058_RS14340at 1227.369 kb on - strand, within HMPREF1058_RS14340at 1227.496 kb on - strand, within HMPREF1058_RS14340at 1227.579 kb on - strand, within HMPREF1058_RS14340at 1227.579 kb on - strand, within HMPREF1058_RS14340at 1227.623 kb on + strand, within HMPREF1058_RS14340at 1227.623 kb on + strand, within HMPREF1058_RS14340at 1227.754 kb on - strand, within HMPREF1058_RS14340at 1227.757 kb on + strand, within HMPREF1058_RS14340at 1227.757 kb on + strand, within HMPREF1058_RS14340at 1227.769 kb on + strand, within HMPREF1058_RS14340at 1227.769 kb on + strand, within HMPREF1058_RS14340at 1227.917 kb on - strand, within HMPREF1058_RS14340at 1227.941 kb on + strand, within HMPREF1058_RS14340at 1227.976 kb on + strand, within HMPREF1058_RS14340at 1227.976 kb on + strand, within HMPREF1058_RS14340at 1228.003 kb on + strand, within HMPREF1058_RS14340at 1228.004 kb on - strand, within HMPREF1058_RS14340at 1228.004 kb on - strand, within HMPREF1058_RS14340at 1228.087 kb on + strand, within HMPREF1058_RS14340at 1228.184 kb on + strand, within HMPREF1058_RS14340at 1228.346 kb on - strand, within HMPREF1058_RS14340at 1228.368 kb on - strand, within HMPREF1058_RS14340at 1228.440 kb on - strand, within HMPREF1058_RS14340at 1228.547 kb on + strand, within HMPREF1058_RS14340at 1228.656 kb on - strand, within HMPREF1058_RS14340at 1228.656 kb on - strandat 1228.660 kb on + strand, within HMPREF1058_RS14340at 1228.664 kb on - strand, within HMPREF1058_RS14340at 1228.800 kb on + strandat 1228.849 kb on + strand, within HMPREF1058_RS14340at 1228.860 kb on + strand, within HMPREF1058_RS14340at 1228.928 kb on + strand, within HMPREF1058_RS14340at 1228.928 kb on + strand, within HMPREF1058_RS14340at 1228.929 kb on - strand, within HMPREF1058_RS14340at 1228.929 kb on - strand, within HMPREF1058_RS14340at 1228.950 kb on + strand, within HMPREF1058_RS14340at 1228.950 kb on + strand, within HMPREF1058_RS14340at 1228.959 kb on + strand, within HMPREF1058_RS14340at 1228.959 kb on + strand, within HMPREF1058_RS14340at 1228.969 kb on - strand, within HMPREF1058_RS14340at 1229.051 kb on + strand, within HMPREF1058_RS14340at 1229.052 kb on - strand, within HMPREF1058_RS14340at 1229.113 kb on - strand, within HMPREF1058_RS14340at 1229.118 kb on + strand, within HMPREF1058_RS14340at 1229.119 kb on - strand, within HMPREF1058_RS14340at 1229.201 kb on + strand, within HMPREF1058_RS14340at 1229.201 kb on + strand, within HMPREF1058_RS14340at 1229.201 kb on + strand, within HMPREF1058_RS14340at 1229.223 kb on + strand, within HMPREF1058_RS14340at 1229.237 kb on + strand, within HMPREF1058_RS14340at 1229.257 kb on - strand, within HMPREF1058_RS14340at 1229.336 kb on - strandat 1229.423 kb on + strandat 1229.424 kb on - strandat 1229.489 kb on + strandat 1229.732 kb on + strandat 1229.733 kb on - strandat 1229.733 kb on - strandat 1229.733 kb on - strandat 1229.739 kb on - strandat 1229.745 kb on - strandat 1229.745 kb on - strandat 1229.764 kb on - strandat 1229.902 kb on + strandat 1229.966 kb on - strandat 1230.029 kb on - strandat 1230.278 kb on - strandat 1230.285 kb on + strand, within HMPREF1058_RS0119435at 1230.286 kb on - strand, within HMPREF1058_RS0119435at 1230.306 kb on + strand, within HMPREF1058_RS0119435at 1230.306 kb on + strand, within HMPREF1058_RS0119435at 1230.307 kb on - strand, within HMPREF1058_RS0119435at 1230.352 kb on - strand, within HMPREF1058_RS0119435at 1230.416 kb on - strand, within HMPREF1058_RS0119435at 1230.417 kb on + strand, within HMPREF1058_RS0119435at 1230.582 kb on - strand, within HMPREF1058_RS0119435

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day4
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1,225,493 + HMPREF1058_RS14345 0.58 -1.4
1,225,494 - HMPREF1058_RS14345 0.58 +1.8
1,225,577 + HMPREF1058_RS14345 0.62 -1.7
1,225,580 - HMPREF1058_RS14345 0.62 -2.1
1,225,580 - HMPREF1058_RS14345 0.62 +0.3
1,225,640 - HMPREF1058_RS14345 0.65 +1.0
1,225,705 - HMPREF1058_RS14345 0.68 +1.1
1,225,735 + HMPREF1058_RS14345 0.69 -0.1
1,225,736 - HMPREF1058_RS14345 0.69 +0.7
1,225,821 + HMPREF1058_RS14345 0.74 -0.1
1,225,833 - HMPREF1058_RS14345 0.74 +0.5
1,225,892 - HMPREF1058_RS14345 0.77 +0.7
1,225,927 + HMPREF1058_RS14345 0.79 -0.3
1,225,927 + HMPREF1058_RS14345 0.79 -2.1
1,225,928 - HMPREF1058_RS14345 0.79 +0.4
1,226,014 - HMPREF1058_RS14345 0.83 +0.8
1,226,014 - HMPREF1058_RS14345 0.83 -0.0
1,226,101 - HMPREF1058_RS14345 0.87 -0.7
1,226,108 + HMPREF1058_RS14345 0.88 +0.1
1,226,109 - HMPREF1058_RS14345 0.88 -0.1
1,226,188 - +1.2
1,226,197 + -3.6
1,226,200 + +1.9
1,226,201 - +0.7
1,226,201 - -2.6
1,226,204 + +0.6
1,226,204 + +1.4
1,226,220 + +1.4
1,226,534 - +1.9
1,226,618 - +1.1
1,226,635 + -2.4
1,226,636 - -0.4
1,227,077 + HMPREF1058_RS14340 0.21 +2.2
1,227,077 + HMPREF1058_RS14340 0.21 +1.2
1,227,077 + HMPREF1058_RS14340 0.21 -0.9
1,227,077 + HMPREF1058_RS14340 0.21 -1.6
1,227,077 + HMPREF1058_RS14340 0.21 +0.5
1,227,077 + HMPREF1058_RS14340 0.21 +0.6
1,227,077 + HMPREF1058_RS14340 0.21 -0.1
1,227,077 + HMPREF1058_RS14340 0.21 +2.1
1,227,078 - HMPREF1058_RS14340 0.21 -0.3
1,227,078 - HMPREF1058_RS14340 0.21 +0.2
1,227,079 + HMPREF1058_RS14340 0.22 +1.8
1,227,112 + HMPREF1058_RS14340 0.23 -2.4
1,227,112 + HMPREF1058_RS14340 0.23 +1.0
1,227,113 - HMPREF1058_RS14340 0.23 +2.8
1,227,170 + HMPREF1058_RS14340 0.24 +0.8
1,227,205 + HMPREF1058_RS14340 0.25 +0.3
1,227,261 - HMPREF1058_RS14340 0.27 +0.2
1,227,336 - HMPREF1058_RS14340 0.29 +0.4
1,227,369 - HMPREF1058_RS14340 0.31 +0.9
1,227,496 - HMPREF1058_RS14340 0.34 -0.1
1,227,579 - HMPREF1058_RS14340 0.37 -0.7
1,227,579 - HMPREF1058_RS14340 0.37 +0.7
1,227,623 + HMPREF1058_RS14340 0.38 +1.0
1,227,623 + HMPREF1058_RS14340 0.38 -0.7
1,227,754 - HMPREF1058_RS14340 0.42 +3.1
1,227,757 + HMPREF1058_RS14340 0.43 +4.3
1,227,757 + HMPREF1058_RS14340 0.43 -0.5
1,227,769 + HMPREF1058_RS14340 0.43 -1.1
1,227,769 + HMPREF1058_RS14340 0.43 +2.2
1,227,917 - HMPREF1058_RS14340 0.48 -1.1
1,227,941 + HMPREF1058_RS14340 0.48 -1.1
1,227,976 + HMPREF1058_RS14340 0.49 +0.1
1,227,976 + HMPREF1058_RS14340 0.49 +2.3
1,228,003 + HMPREF1058_RS14340 0.50 +1.3
1,228,004 - HMPREF1058_RS14340 0.50 +0.0
1,228,004 - HMPREF1058_RS14340 0.50 +1.9
1,228,087 + HMPREF1058_RS14340 0.53 +2.1
1,228,184 + HMPREF1058_RS14340 0.56 +0.6
1,228,346 - HMPREF1058_RS14340 0.61 +2.3
1,228,368 - HMPREF1058_RS14340 0.61 +1.4
1,228,440 - HMPREF1058_RS14340 0.64 +1.2
1,228,547 + HMPREF1058_RS14340 0.67 +2.0
1,228,656 - HMPREF1058_RS14340 0.70 +0.9
1,228,656 - -0.1
1,228,660 + HMPREF1058_RS14340 0.71 -2.1
1,228,664 - HMPREF1058_RS14340 0.71 +0.9
1,228,800 + -1.1
1,228,849 + HMPREF1058_RS14340 0.76 +1.7
1,228,860 + HMPREF1058_RS14340 0.77 -0.4
1,228,928 + HMPREF1058_RS14340 0.79 +1.6
1,228,928 + HMPREF1058_RS14340 0.79 +0.1
1,228,929 - HMPREF1058_RS14340 0.79 +0.1
1,228,929 - HMPREF1058_RS14340 0.79 +3.0
1,228,950 + HMPREF1058_RS14340 0.80 +1.9
1,228,950 + HMPREF1058_RS14340 0.80 -0.7
1,228,959 + HMPREF1058_RS14340 0.80 -1.4
1,228,959 + HMPREF1058_RS14340 0.80 -0.2
1,228,969 - HMPREF1058_RS14340 0.80 +1.4
1,229,051 + HMPREF1058_RS14340 0.83 +0.6
1,229,052 - HMPREF1058_RS14340 0.83 -0.4
1,229,113 - HMPREF1058_RS14340 0.85 +2.2
1,229,118 + HMPREF1058_RS14340 0.85 +1.5
1,229,119 - HMPREF1058_RS14340 0.85 -1.4
1,229,201 + HMPREF1058_RS14340 0.87 -0.6
1,229,201 + HMPREF1058_RS14340 0.87 -0.1
1,229,201 + HMPREF1058_RS14340 0.87 +0.5
1,229,223 + HMPREF1058_RS14340 0.88 -0.1
1,229,237 + HMPREF1058_RS14340 0.88 +1.9
1,229,257 - HMPREF1058_RS14340 0.89 +1.2
1,229,336 - -0.1
1,229,423 + +0.7
1,229,424 - +0.1
1,229,489 + -0.1
1,229,732 + -0.3
1,229,733 - -4.0
1,229,733 - -2.5
1,229,733 - -1.1
1,229,739 - -1.4
1,229,745 - -2.2
1,229,745 - -1.1
1,229,764 - -0.1
1,229,902 + +0.3
1,229,966 - -2.4
1,230,029 - -0.1
1,230,278 - +0.4
1,230,285 + HMPREF1058_RS0119435 0.10 +2.2
1,230,286 - HMPREF1058_RS0119435 0.10 +3.4
1,230,306 + HMPREF1058_RS0119435 0.13 -0.1
1,230,306 + HMPREF1058_RS0119435 0.13 +1.3
1,230,307 - HMPREF1058_RS0119435 0.13 +0.5
1,230,352 - HMPREF1058_RS0119435 0.19 -0.7
1,230,416 - HMPREF1058_RS0119435 0.27 +2.8
1,230,417 + HMPREF1058_RS0119435 0.27 -1.1
1,230,582 - HMPREF1058_RS0119435 0.48 +1.3

Or see this region's nucleotide sequence