Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS02005

Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse14; day3

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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_RS02015 and HMPREF1058_RS02010 are separated by 207 nucleotidesHMPREF1058_RS02010 and HMPREF1058_RS02005 are separated by 90 nucleotidesHMPREF1058_RS02005 and HMPREF1058_RS02000 are separated by 146 nucleotidesHMPREF1058_RS02000 and HMPREF1058_RS01995 are separated by 56 nucleotidesHMPREF1058_RS01995 and HMPREF1058_RS01990 are separated by 183 nucleotides HMPREF1058_RS02015: HMPREF1058_RS02015 - ASCH domain-containing protein, at 920 to 1,465 _RS02015 HMPREF1058_RS02010: HMPREF1058_RS02010 - hypothetical protein, at 1,673 to 1,855 _RS02010 HMPREF1058_RS02005: HMPREF1058_RS02005 - hypothetical protein, at 1,946 to 2,383 _RS02005 HMPREF1058_RS02000: HMPREF1058_RS02000 - type II toxin-antitoxin system HicA family toxin, at 2,530 to 2,715 _RS02000 HMPREF1058_RS01995: HMPREF1058_RS01995 - hypothetical protein, at 2,772 to 3,176 _RS01995 HMPREF1058_RS01990: HMPREF1058_RS01990 - hypothetical protein, at 3,360 to 3,746 _RS01990 Position (kb) 1 2 3Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 0.991 kb on + strand, within HMPREF1058_RS02015at 1.014 kb on - strand, within HMPREF1058_RS02015at 1.029 kb on + strand, within HMPREF1058_RS02015at 1.061 kb on + strand, within HMPREF1058_RS02015at 1.062 kb on - strand, within HMPREF1058_RS02015at 1.074 kb on - strand, within HMPREF1058_RS02015at 1.087 kb on + strand, within HMPREF1058_RS02015at 1.291 kb on - strand, within HMPREF1058_RS02015at 1.329 kb on + strand, within HMPREF1058_RS02015at 1.330 kb on - strand, within HMPREF1058_RS02015at 1.353 kb on + strand, within HMPREF1058_RS02015at 1.359 kb on + strandat 1.360 kb on - strand, within HMPREF1058_RS02015at 1.375 kb on + strand, within HMPREF1058_RS02015at 1.376 kb on - strand, within HMPREF1058_RS02015at 1.405 kb on + strand, within HMPREF1058_RS02015at 1.406 kb on - strand, within HMPREF1058_RS02015at 1.411 kb on + strandat 1.412 kb on - strandat 1.415 kb on - strandat 1.507 kb on - strandat 1.539 kb on + strandat 1.540 kb on - strandat 1.650 kb on + strandat 1.650 kb on + strandat 1.661 kb on - strandat 1.666 kb on + strandat 1.712 kb on - strand, within HMPREF1058_RS02010at 1.747 kb on - strand, within HMPREF1058_RS02010at 1.771 kb on - strand, within HMPREF1058_RS02010at 1.796 kb on + strand, within HMPREF1058_RS02010at 1.797 kb on - strand, within HMPREF1058_RS02010at 1.798 kb on + strand, within HMPREF1058_RS02010at 1.798 kb on + strand, within HMPREF1058_RS02010at 1.799 kb on - strand, within HMPREF1058_RS02010at 1.809 kb on - strand, within HMPREF1058_RS02010at 1.917 kb on - strandat 1.961 kb on - strandat 2.072 kb on + strand, within HMPREF1058_RS02005at 2.119 kb on + strand, within HMPREF1058_RS02005at 2.119 kb on + strand, within HMPREF1058_RS02005at 2.258 kb on - strand, within HMPREF1058_RS02005at 2.325 kb on + strand, within HMPREF1058_RS02005at 2.325 kb on + strand, within HMPREF1058_RS02005at 2.330 kb on + strand, within HMPREF1058_RS02005at 2.331 kb on - strand, within HMPREF1058_RS02005at 2.331 kb on - strand, within HMPREF1058_RS02005at 2.421 kb on - strandat 2.475 kb on + strandat 2.601 kb on + strand, within HMPREF1058_RS02000at 2.602 kb on - strand, within HMPREF1058_RS02000at 2.605 kb on + strand, within HMPREF1058_RS02000at 2.957 kb on + strand, within HMPREF1058_RS01995at 2.979 kb on + strand, within HMPREF1058_RS01995at 2.983 kb on + strand, within HMPREF1058_RS01995at 2.985 kb on + strand, within HMPREF1058_RS01995at 3.078 kb on + strand, within HMPREF1058_RS01995at 3.135 kb on + strand, within HMPREF1058_RS01995at 3.135 kb on + strand, within HMPREF1058_RS01995at 3.253 kb on - strandat 3.281 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse14; day3
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991 + HMPREF1058_RS02015 0.13 +1.3
1,014 - HMPREF1058_RS02015 0.17 -0.2
1,029 + HMPREF1058_RS02015 0.20 +0.1
1,061 + HMPREF1058_RS02015 0.26 -0.8
1,062 - HMPREF1058_RS02015 0.26 -1.6
1,074 - HMPREF1058_RS02015 0.28 +1.2
1,087 + HMPREF1058_RS02015 0.31 -0.0
1,291 - HMPREF1058_RS02015 0.68 +0.1
1,329 + HMPREF1058_RS02015 0.75 -0.2
1,330 - HMPREF1058_RS02015 0.75 -0.1
1,353 + HMPREF1058_RS02015 0.79 -2.4
1,359 + +1.9
1,360 - HMPREF1058_RS02015 0.81 +0.5
1,375 + HMPREF1058_RS02015 0.83 -0.3
1,376 - HMPREF1058_RS02015 0.84 +0.2
1,405 + HMPREF1058_RS02015 0.89 +0.9
1,406 - HMPREF1058_RS02015 0.89 +0.6
1,411 + +0.9
1,412 - +0.3
1,415 - +2.1
1,507 - -1.3
1,539 + +1.4
1,540 - +0.2
1,650 + -0.1
1,650 + +0.7
1,661 - +0.9
1,666 + -2.8
1,712 - HMPREF1058_RS02010 0.21 -0.5
1,747 - HMPREF1058_RS02010 0.40 +0.4
1,771 - HMPREF1058_RS02010 0.54 -0.3
1,796 + HMPREF1058_RS02010 0.67 +0.1
1,797 - HMPREF1058_RS02010 0.68 -0.1
1,798 + HMPREF1058_RS02010 0.68 +0.2
1,798 + HMPREF1058_RS02010 0.68 -0.3
1,799 - HMPREF1058_RS02010 0.69 -1.1
1,809 - HMPREF1058_RS02010 0.74 -0.1
1,917 - -0.1
1,961 - -0.4
2,072 + HMPREF1058_RS02005 0.29 +0.3
2,119 + HMPREF1058_RS02005 0.39 +0.3
2,119 + HMPREF1058_RS02005 0.39 +0.5
2,258 - HMPREF1058_RS02005 0.71 -3.3
2,325 + HMPREF1058_RS02005 0.87 +1.8
2,325 + HMPREF1058_RS02005 0.87 +1.4
2,330 + HMPREF1058_RS02005 0.88 +0.0
2,331 - HMPREF1058_RS02005 0.88 +0.0
2,331 - HMPREF1058_RS02005 0.88 -1.4
2,421 - -0.2
2,475 + -1.3
2,601 + HMPREF1058_RS02000 0.38 -0.4
2,602 - HMPREF1058_RS02000 0.39 +0.1
2,605 + HMPREF1058_RS02000 0.40 +0.1
2,957 + HMPREF1058_RS01995 0.46 +1.0
2,979 + HMPREF1058_RS01995 0.51 -0.3
2,983 + HMPREF1058_RS01995 0.52 +1.3
2,985 + HMPREF1058_RS01995 0.53 +0.1
3,078 + HMPREF1058_RS01995 0.76 +0.3
3,135 + HMPREF1058_RS01995 0.90 -2.3
3,135 + HMPREF1058_RS01995 0.90 -2.3
3,253 - +0.3
3,281 - +0.2

Or see this region's nucleotide sequence