Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS06410

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse7; 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_RS06425 and HMPREF1058_RS06420 are separated by 154 nucleotidesHMPREF1058_RS06420 and HMPREF1058_RS06415 are separated by 39 nucleotidesHMPREF1058_RS06415 and HMPREF1058_RS06410 are separated by 83 nucleotidesHMPREF1058_RS06410 and HMPREF1058_RS06405 are separated by 131 nucleotides HMPREF1058_RS06425: HMPREF1058_RS06425 - winged helix-turn-helix domain-containing protein, at 481,709 to 481,912 _RS06425 HMPREF1058_RS06420: HMPREF1058_RS06420 - type II toxin-antitoxin system HicA family toxin, at 482,067 to 482,255 _RS06420 HMPREF1058_RS06415: HMPREF1058_RS06415 - antitoxin HicB, at 482,295 to 482,687 _RS06415 HMPREF1058_RS06410: HMPREF1058_RS06410 - elongation factor 4, at 482,771 to 484,552 _RS06410 HMPREF1058_RS06405: HMPREF1058_RS06405 - Na+/H+ antiporter NhaA, at 484,684 to 486,024 _RS06405 Position (kb) 482 483 484 485Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3at 481.861 kb on + strand, within HMPREF1058_RS06425at 481.861 kb on + strand, within HMPREF1058_RS06425at 481.911 kb on - strandat 481.987 kb on + strandat 481.999 kb on - strandat 482.074 kb on - strandat 482.122 kb on + strand, within HMPREF1058_RS06420at 482.122 kb on + strand, within HMPREF1058_RS06420at 482.220 kb on + strand, within HMPREF1058_RS06420at 482.220 kb on + strand, within HMPREF1058_RS06420at 482.220 kb on + strand, within HMPREF1058_RS06420at 482.220 kb on + strand, within HMPREF1058_RS06420at 482.221 kb on - strand, within HMPREF1058_RS06420at 482.221 kb on - strand, within HMPREF1058_RS06420at 482.519 kb on + strand, within HMPREF1058_RS06415at 482.674 kb on + strandat 482.755 kb on + strandat 482.799 kb on + strandat 482.806 kb on + strandat 482.806 kb on + strandat 482.806 kb on + strandat 482.808 kb on + strandat 482.808 kb on + strandat 482.918 kb on - strandat 482.918 kb on - strandat 482.973 kb on - strand, within HMPREF1058_RS06410at 482.977 kb on - strand, within HMPREF1058_RS06410at 483.232 kb on + strand, within HMPREF1058_RS06410at 483.455 kb on + strand, within HMPREF1058_RS06410at 483.532 kb on + strand, within HMPREF1058_RS06410at 483.664 kb on + strand, within HMPREF1058_RS06410at 483.841 kb on + strand, within HMPREF1058_RS06410at 484.157 kb on + strand, within HMPREF1058_RS06410at 484.172 kb on + strand, within HMPREF1058_RS06410at 484.294 kb on + strand, within HMPREF1058_RS06410at 484.295 kb on - strand, within HMPREF1058_RS06410at 484.372 kb on + strand, within HMPREF1058_RS06410at 484.477 kb on + strandat 484.562 kb on - strandat 484.738 kb on + strandat 484.743 kb on + strandat 484.744 kb on - strandat 484.744 kb on - strandat 484.746 kb on + strandat 484.816 kb on - strandat 484.820 kb on - strand, within HMPREF1058_RS06405at 484.820 kb on - strand, within HMPREF1058_RS06405at 484.820 kb on - strand, within HMPREF1058_RS06405at 484.961 kb on + strand, within HMPREF1058_RS06405at 485.059 kb on + strand, within HMPREF1058_RS06405at 485.063 kb on - strand, within HMPREF1058_RS06405at 485.347 kb on - strandat 485.365 kb on - strand, within HMPREF1058_RS06405at 485.450 kb on - strand, within HMPREF1058_RS06405at 485.460 kb on + strand, within HMPREF1058_RS06405at 485.460 kb on + strand, within HMPREF1058_RS06405at 485.460 kb on + strand, within HMPREF1058_RS06405at 485.460 kb on + strand, within HMPREF1058_RS06405at 485.460 kb on + strand, within HMPREF1058_RS06405at 485.461 kb on - strand, within HMPREF1058_RS06405at 485.461 kb on - strand, within HMPREF1058_RS06405at 485.464 kb on + strand, within HMPREF1058_RS06405at 485.465 kb on - strand, within HMPREF1058_RS06405at 485.465 kb on - strand, within HMPREF1058_RS06405

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse7; day4
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481,861 + HMPREF1058_RS06425 0.75 +1.3
481,861 + HMPREF1058_RS06425 0.75 -1.0
481,911 - +1.6
481,987 + -1.0
481,999 - +1.6
482,074 - +0.6
482,122 + HMPREF1058_RS06420 0.29 -0.2
482,122 + HMPREF1058_RS06420 0.29 +1.0
482,220 + HMPREF1058_RS06420 0.81 -0.6
482,220 + HMPREF1058_RS06420 0.81 -0.9
482,220 + HMPREF1058_RS06420 0.81 +0.1
482,220 + HMPREF1058_RS06420 0.81 +0.6
482,221 - HMPREF1058_RS06420 0.81 +0.6
482,221 - HMPREF1058_RS06420 0.81 +0.6
482,519 + HMPREF1058_RS06415 0.57 -1.0
482,674 + -2.0
482,755 + -0.7
482,799 + -1.0
482,806 + -2.0
482,806 + -0.0
482,806 + -1.0
482,808 + -2.3
482,808 + -2.6
482,918 - -1.6
482,918 - -1.0
482,973 - HMPREF1058_RS06410 0.11 -1.0
482,977 - HMPREF1058_RS06410 0.12 -0.0
483,232 + HMPREF1058_RS06410 0.26 -2.0
483,455 + HMPREF1058_RS06410 0.38 -2.6
483,532 + HMPREF1058_RS06410 0.43 -1.6
483,664 + HMPREF1058_RS06410 0.50 -1.6
483,841 + HMPREF1058_RS06410 0.60 -3.3
484,157 + HMPREF1058_RS06410 0.78 -2.0
484,172 + HMPREF1058_RS06410 0.79 -1.0
484,294 + HMPREF1058_RS06410 0.85 -3.2
484,295 - HMPREF1058_RS06410 0.86 -1.0
484,372 + HMPREF1058_RS06410 0.90 -0.0
484,477 + -2.3
484,562 - -1.0
484,738 + -2.6
484,743 + +1.6
484,744 - -0.0
484,744 - +1.2
484,746 + +3.3
484,816 - +1.0
484,820 - HMPREF1058_RS06405 0.10 +1.6
484,820 - HMPREF1058_RS06405 0.10 +2.0
484,820 - HMPREF1058_RS06405 0.10 +0.4
484,961 + HMPREF1058_RS06405 0.21 -0.0
485,059 + HMPREF1058_RS06405 0.28 -1.6
485,063 - HMPREF1058_RS06405 0.28 -0.3
485,347 - -1.6
485,365 - HMPREF1058_RS06405 0.51 -2.2
485,450 - HMPREF1058_RS06405 0.57 +1.6
485,460 + HMPREF1058_RS06405 0.58 +0.3
485,460 + HMPREF1058_RS06405 0.58 -1.4
485,460 + HMPREF1058_RS06405 0.58 +2.7
485,460 + HMPREF1058_RS06405 0.58 +1.4
485,460 + HMPREF1058_RS06405 0.58 +0.6
485,461 - HMPREF1058_RS06405 0.58 -0.6
485,461 - HMPREF1058_RS06405 0.58 +1.7
485,464 + HMPREF1058_RS06405 0.58 +2.0
485,465 - HMPREF1058_RS06405 0.58 -2.3
485,465 - HMPREF1058_RS06405 0.58 -0.8

Or see this region's nucleotide sequence