Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS12175

Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse16; day9

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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_RS12190 and HMPREF1058_RS12185 are separated by 2 nucleotidesHMPREF1058_RS12185 and HMPREF1058_RS12180 are separated by 138 nucleotidesHMPREF1058_RS12180 and HMPREF1058_RS12175 overlap by 40 nucleotidesHMPREF1058_RS12175 and HMPREF1058_RS12170 are separated by 213 nucleotidesHMPREF1058_RS12170 and HMPREF1058_RS12165 are separated by 20 nucleotides HMPREF1058_RS12190: HMPREF1058_RS12190 - transcription termination/antitermination protein NusA, at 181,874 to 183,130 _RS12190 HMPREF1058_RS12185: HMPREF1058_RS12185 - ribosome assembly cofactor RimP, at 183,133 to 183,600 _RS12185 HMPREF1058_RS12180: HMPREF1058_RS12180 - hypothetical protein, at 183,739 to 184,158 _RS12180 HMPREF1058_RS12175: HMPREF1058_RS12175 - MFS transporter AraJ, at 184,119 to 185,279 _RS12175 HMPREF1058_RS12170: HMPREF1058_RS12170 - hypothetical protein, at 185,493 to 185,741 _RS12170 HMPREF1058_RS12165: HMPREF1058_RS12165 - radical SAM protein, at 185,762 to 186,832 _RS12165 Position (kb) 184 185 186Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3 4 5 6at 183.377 kb on - strand, within HMPREF1058_RS12185at 183.677 kb on - strandat 183.702 kb on - strandat 183.731 kb on - strandat 183.732 kb on + strandat 183.744 kb on + strandat 183.779 kb on + strandat 183.780 kb on - strandat 183.789 kb on + strand, within HMPREF1058_RS12180at 183.817 kb on - strand, within HMPREF1058_RS12180at 183.834 kb on + strand, within HMPREF1058_RS12180at 183.869 kb on + strand, within HMPREF1058_RS12180at 183.877 kb on + strand, within HMPREF1058_RS12180at 183.877 kb on + strand, within HMPREF1058_RS12180at 183.877 kb on + strand, within HMPREF1058_RS12180at 183.896 kb on + strand, within HMPREF1058_RS12180at 183.927 kb on + strand, within HMPREF1058_RS12180at 183.930 kb on - strand, within HMPREF1058_RS12180at 183.930 kb on - strand, within HMPREF1058_RS12180at 184.018 kb on - strand, within HMPREF1058_RS12180at 184.023 kb on - strand, within HMPREF1058_RS12180at 184.120 kb on + strandat 184.123 kb on - strandat 184.186 kb on - strandat 184.236 kb on + strand, within HMPREF1058_RS12175at 184.237 kb on - strand, within HMPREF1058_RS12175at 184.344 kb on + strand, within HMPREF1058_RS12175at 184.345 kb on - strand, within HMPREF1058_RS12175at 184.382 kb on + strand, within HMPREF1058_RS12175at 184.383 kb on - strand, within HMPREF1058_RS12175at 184.383 kb on - strand, within HMPREF1058_RS12175at 184.386 kb on + strand, within HMPREF1058_RS12175at 184.386 kb on + strand, within HMPREF1058_RS12175at 184.387 kb on - strand, within HMPREF1058_RS12175at 184.387 kb on - strand, within HMPREF1058_RS12175at 184.387 kb on - strand, within HMPREF1058_RS12175at 184.387 kb on - strand, within HMPREF1058_RS12175at 184.388 kb on + strand, within HMPREF1058_RS12175at 184.388 kb on + strand, within HMPREF1058_RS12175at 184.571 kb on + strand, within HMPREF1058_RS12175at 184.571 kb on + strand, within HMPREF1058_RS12175at 184.618 kb on + strand, within HMPREF1058_RS12175at 184.619 kb on - strand, within HMPREF1058_RS12175at 184.619 kb on - strand, within HMPREF1058_RS12175at 184.619 kb on - strand, within HMPREF1058_RS12175at 184.655 kb on + strand, within HMPREF1058_RS12175at 184.721 kb on + strand, within HMPREF1058_RS12175at 184.763 kb on - strand, within HMPREF1058_RS12175at 184.794 kb on - strand, within HMPREF1058_RS12175at 184.821 kb on + strand, within HMPREF1058_RS12175at 184.821 kb on + strand, within HMPREF1058_RS12175at 184.823 kb on + strand, within HMPREF1058_RS12175at 184.823 kb on + strand, within HMPREF1058_RS12175at 184.823 kb on + strand, within HMPREF1058_RS12175at 184.824 kb on - strand, within HMPREF1058_RS12175at 184.824 kb on - strand, within HMPREF1058_RS12175at 185.045 kb on + strand, within HMPREF1058_RS12175at 185.048 kb on - strand, within HMPREF1058_RS12175at 185.052 kb on - strand, within HMPREF1058_RS12175at 185.072 kb on + strand, within HMPREF1058_RS12175at 185.072 kb on + strand, within HMPREF1058_RS12175at 185.133 kb on + strand, within HMPREF1058_RS12175at 185.172 kb on - strandat 185.175 kb on + strandat 185.176 kb on - strandat 185.176 kb on - strandat 185.177 kb on + strandat 185.217 kb on + strandat 185.322 kb on + strandat 185.383 kb on - strandat 185.436 kb on - strandat 185.659 kb on - strand, within HMPREF1058_RS12170at 185.660 kb on + strand, within HMPREF1058_RS12170at 185.661 kb on - strand, within HMPREF1058_RS12170at 185.769 kb on - strandat 185.799 kb on + strandat 185.840 kb on + strandat 185.842 kb on + strandat 185.843 kb on - strandat 185.867 kb on - strandat 185.874 kb on + strand, within HMPREF1058_RS12165at 185.878 kb on + strand, within HMPREF1058_RS12165at 185.878 kb on + strand, within HMPREF1058_RS12165at 185.879 kb on - strand, within HMPREF1058_RS12165at 185.906 kb on - strand, within HMPREF1058_RS12165at 185.906 kb on - strand, within HMPREF1058_RS12165at 185.906 kb on - strand, within HMPREF1058_RS12165at 185.968 kb on + strand, within HMPREF1058_RS12165at 185.968 kb on + strand, within HMPREF1058_RS12165at 185.983 kb on + strand, within HMPREF1058_RS12165at 185.998 kb on - strand, within HMPREF1058_RS12165at 186.019 kb on - strand, within HMPREF1058_RS12165at 186.021 kb on - strand, within HMPREF1058_RS12165at 186.023 kb on - strand, within HMPREF1058_RS12165at 186.023 kb on - strand, within HMPREF1058_RS12165at 186.024 kb on + strand, within HMPREF1058_RS12165at 186.024 kb on + strand, within HMPREF1058_RS12165at 186.072 kb on + strand, within HMPREF1058_RS12165at 186.073 kb on - strand, within HMPREF1058_RS12165at 186.104 kb on - strand, within HMPREF1058_RS12165at 186.104 kb on - strand, within HMPREF1058_RS12165at 186.216 kb on + strand, within HMPREF1058_RS12165at 186.219 kb on + strand, within HMPREF1058_RS12165at 186.219 kb on + strand, within HMPREF1058_RS12165at 186.219 kb on + strand, within HMPREF1058_RS12165at 186.227 kb on - strand, within HMPREF1058_RS12165at 186.254 kb on + strand, within HMPREF1058_RS12165

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse16; day9
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183,377 - HMPREF1058_RS12185 0.52 +1.1
183,677 - -0.3
183,702 - +0.7
183,731 - +1.1
183,732 + +0.1
183,744 + +1.1
183,779 + -1.6
183,780 - -0.7
183,789 + HMPREF1058_RS12180 0.12 -1.6
183,817 - HMPREF1058_RS12180 0.19 -0.3
183,834 + HMPREF1058_RS12180 0.23 +0.6
183,869 + HMPREF1058_RS12180 0.31 +0.2
183,877 + HMPREF1058_RS12180 0.33 -0.1
183,877 + HMPREF1058_RS12180 0.33 -0.6
183,877 + HMPREF1058_RS12180 0.33 +1.5
183,896 + HMPREF1058_RS12180 0.37 +0.0
183,927 + HMPREF1058_RS12180 0.45 +0.6
183,930 - HMPREF1058_RS12180 0.45 -0.3
183,930 - HMPREF1058_RS12180 0.45 -1.7
184,018 - HMPREF1058_RS12180 0.66 -0.9
184,023 - HMPREF1058_RS12180 0.68 -1.6
184,120 + +0.1
184,123 - +0.3
184,186 - -1.2
184,236 + HMPREF1058_RS12175 0.10 -1.3
184,237 - HMPREF1058_RS12175 0.10 -0.4
184,344 + HMPREF1058_RS12175 0.19 +0.3
184,345 - HMPREF1058_RS12175 0.19 -2.4
184,382 + HMPREF1058_RS12175 0.23 +0.9
184,383 - HMPREF1058_RS12175 0.23 -0.5
184,383 - HMPREF1058_RS12175 0.23 -0.7
184,386 + HMPREF1058_RS12175 0.23 -0.2
184,386 + HMPREF1058_RS12175 0.23 +0.4
184,387 - HMPREF1058_RS12175 0.23 +0.2
184,387 - HMPREF1058_RS12175 0.23 -1.3
184,387 - HMPREF1058_RS12175 0.23 -1.9
184,387 - HMPREF1058_RS12175 0.23 -0.4
184,388 + HMPREF1058_RS12175 0.23 +6.1
184,388 + HMPREF1058_RS12175 0.23 +1.3
184,571 + HMPREF1058_RS12175 0.39 -2.1
184,571 + HMPREF1058_RS12175 0.39 +0.3
184,618 + HMPREF1058_RS12175 0.43 +0.5
184,619 - HMPREF1058_RS12175 0.43 +0.1
184,619 - HMPREF1058_RS12175 0.43 -2.6
184,619 - HMPREF1058_RS12175 0.43 +3.9
184,655 + HMPREF1058_RS12175 0.46 -0.5
184,721 + HMPREF1058_RS12175 0.52 +0.3
184,763 - HMPREF1058_RS12175 0.55 -0.5
184,794 - HMPREF1058_RS12175 0.58 +0.5
184,821 + HMPREF1058_RS12175 0.60 -0.6
184,821 + HMPREF1058_RS12175 0.60 -0.4
184,823 + HMPREF1058_RS12175 0.61 +0.3
184,823 + HMPREF1058_RS12175 0.61 -0.4
184,823 + HMPREF1058_RS12175 0.61 -0.0
184,824 - HMPREF1058_RS12175 0.61 +0.5
184,824 - HMPREF1058_RS12175 0.61 -0.3
185,045 + HMPREF1058_RS12175 0.80 +2.1
185,048 - HMPREF1058_RS12175 0.80 -0.1
185,052 - HMPREF1058_RS12175 0.80 +0.3
185,072 + HMPREF1058_RS12175 0.82 -1.0
185,072 + HMPREF1058_RS12175 0.82 -1.9
185,133 + HMPREF1058_RS12175 0.87 +1.4
185,172 - +0.0
185,175 + -1.1
185,176 - -0.6
185,176 - +0.1
185,177 + -3.4
185,217 + -0.8
185,322 + -1.1
185,383 - -0.5
185,436 - +0.6
185,659 - HMPREF1058_RS12170 0.67 -1.8
185,660 + HMPREF1058_RS12170 0.67 +1.1
185,661 - HMPREF1058_RS12170 0.67 -2.0
185,769 - +0.4
185,799 + -0.4
185,840 + -0.3
185,842 + -0.1
185,843 - -1.0
185,867 - +0.5
185,874 + HMPREF1058_RS12165 0.10 -1.0
185,878 + HMPREF1058_RS12165 0.11 +3.2
185,878 + HMPREF1058_RS12165 0.11 -2.2
185,879 - HMPREF1058_RS12165 0.11 +0.3
185,906 - HMPREF1058_RS12165 0.13 -2.1
185,906 - HMPREF1058_RS12165 0.13 -2.2
185,906 - HMPREF1058_RS12165 0.13 +0.3
185,968 + HMPREF1058_RS12165 0.19 +0.3
185,968 + HMPREF1058_RS12165 0.19 -0.4
185,983 + HMPREF1058_RS12165 0.21 +0.7
185,998 - HMPREF1058_RS12165 0.22 -0.6
186,019 - HMPREF1058_RS12165 0.24 -2.5
186,021 - HMPREF1058_RS12165 0.24 -1.3
186,023 - HMPREF1058_RS12165 0.24 -3.3
186,023 - HMPREF1058_RS12165 0.24 -1.0
186,024 + HMPREF1058_RS12165 0.24 +0.4
186,024 + HMPREF1058_RS12165 0.24 +0.0
186,072 + HMPREF1058_RS12165 0.29 +0.8
186,073 - HMPREF1058_RS12165 0.29 +0.3
186,104 - HMPREF1058_RS12165 0.32 -1.2
186,104 - HMPREF1058_RS12165 0.32 +0.7
186,216 + HMPREF1058_RS12165 0.42 -0.5
186,219 + HMPREF1058_RS12165 0.43 -1.7
186,219 + HMPREF1058_RS12165 0.43 +0.7
186,219 + HMPREF1058_RS12165 0.43 +3.2
186,227 - HMPREF1058_RS12165 0.43 +2.5
186,254 + HMPREF1058_RS12165 0.46 +0.5

Or see this region's nucleotide sequence