Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS01585

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; 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_RS01590 and HMPREF1058_RS01585 are separated by 325 nucleotidesHMPREF1058_RS01585 and HMPREF1058_RS01580 are separated by 101 nucleotidesHMPREF1058_RS01580 and HMPREF1058_RS01575 overlap by 38 nucleotides HMPREF1058_RS01590: HMPREF1058_RS01590 - glucuronate isomerase, at 85,150 to 86,556 _RS01590 HMPREF1058_RS01585: HMPREF1058_RS01585 - tagaturonate reductase, at 86,882 to 88,321 _RS01585 HMPREF1058_RS01580: HMPREF1058_RS01580 - hypothetical protein, at 88,423 to 88,836 _RS01580 HMPREF1058_RS01575: HMPREF1058_RS01575 - precorrin-2 C(20)-methyltransferase, at 88,799 to 89,527 _RS01575 Position (kb) 86 87 88 89Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2at 85.937 kb on - strand, within HMPREF1058_RS01590at 85.958 kb on + strand, within HMPREF1058_RS01590at 85.958 kb on + strand, within HMPREF1058_RS01590at 85.959 kb on - strand, within HMPREF1058_RS01590at 85.959 kb on - strand, within HMPREF1058_RS01590at 86.092 kb on - strandat 86.252 kb on + strand, within HMPREF1058_RS01590at 86.253 kb on - strand, within HMPREF1058_RS01590at 86.253 kb on - strand, within HMPREF1058_RS01590at 86.271 kb on + strand, within HMPREF1058_RS01590at 86.272 kb on - strand, within HMPREF1058_RS01590at 86.273 kb on + strand, within HMPREF1058_RS01590at 86.376 kb on + strand, within HMPREF1058_RS01590at 86.377 kb on - strand, within HMPREF1058_RS01590at 86.379 kb on - strand, within HMPREF1058_RS01590at 86.469 kb on + strandat 86.869 kb on + strandat 86.871 kb on + strandat 86.987 kb on + strandat 86.988 kb on - strandat 86.988 kb on - strandat 86.988 kb on - strandat 87.094 kb on - strand, within HMPREF1058_RS01585at 87.094 kb on - strand, within HMPREF1058_RS01585at 87.229 kb on + strand, within HMPREF1058_RS01585at 87.236 kb on - strand, within HMPREF1058_RS01585at 87.437 kb on + strand, within HMPREF1058_RS01585at 87.438 kb on - strand, within HMPREF1058_RS01585at 87.500 kb on + strand, within HMPREF1058_RS01585at 87.500 kb on + strand, within HMPREF1058_RS01585at 87.501 kb on - strand, within HMPREF1058_RS01585at 87.707 kb on + strand, within HMPREF1058_RS01585at 87.767 kb on + strand, within HMPREF1058_RS01585at 87.825 kb on - strand, within HMPREF1058_RS01585at 87.832 kb on + strand, within HMPREF1058_RS01585at 87.977 kb on + strand, within HMPREF1058_RS01585at 87.977 kb on + strand, within HMPREF1058_RS01585at 88.010 kb on + strand, within HMPREF1058_RS01585at 88.077 kb on - strand, within HMPREF1058_RS01585at 88.257 kb on + strandat 88.277 kb on - strandat 88.292 kb on - strandat 88.313 kb on - strandat 88.374 kb on + strandat 88.403 kb on - strandat 88.412 kb on - strandat 88.473 kb on + strand, within HMPREF1058_RS01580at 88.473 kb on + strand, within HMPREF1058_RS01580at 88.474 kb on - strand, within HMPREF1058_RS01580at 88.497 kb on + strand, within HMPREF1058_RS01580at 88.498 kb on - strand, within HMPREF1058_RS01580at 88.526 kb on - strand, within HMPREF1058_RS01580at 88.578 kb on - strand, within HMPREF1058_RS01580at 88.588 kb on + strand, within HMPREF1058_RS01580at 88.594 kb on - strand, within HMPREF1058_RS01580at 88.620 kb on + strand, within HMPREF1058_RS01580at 88.866 kb on - strandat 88.966 kb on - strand, within HMPREF1058_RS01575at 88.966 kb on - strand, within HMPREF1058_RS01575at 88.976 kb on + strand, within HMPREF1058_RS01575at 88.976 kb on + strand, within HMPREF1058_RS01575at 88.976 kb on + strand, within HMPREF1058_RS01575at 89.031 kb on + strand, within HMPREF1058_RS01575at 89.031 kb on + strand, within HMPREF1058_RS01575at 89.032 kb on - strand, within HMPREF1058_RS01575at 89.054 kb on - strand, within HMPREF1058_RS01575at 89.103 kb on - strand, within HMPREF1058_RS01575at 89.189 kb on + strand, within HMPREF1058_RS01575at 89.190 kb on - strand, within HMPREF1058_RS01575at 89.194 kb on - strand, within HMPREF1058_RS01575at 89.194 kb on - strand, within HMPREF1058_RS01575

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day4
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85,937 - HMPREF1058_RS01590 0.56 -1.4
85,958 + HMPREF1058_RS01590 0.57 -1.1
85,958 + HMPREF1058_RS01590 0.57 -0.3
85,959 - HMPREF1058_RS01590 0.57 -2.2
85,959 - HMPREF1058_RS01590 0.57 -1.3
86,092 - -0.8
86,252 + HMPREF1058_RS01590 0.78 -2.3
86,253 - HMPREF1058_RS01590 0.78 -2.1
86,253 - HMPREF1058_RS01590 0.78 -2.1
86,271 + HMPREF1058_RS01590 0.80 -2.3
86,272 - HMPREF1058_RS01590 0.80 -0.8
86,273 + HMPREF1058_RS01590 0.80 -0.8
86,376 + HMPREF1058_RS01590 0.87 -1.3
86,377 - HMPREF1058_RS01590 0.87 -0.9
86,379 - HMPREF1058_RS01590 0.87 -4.0
86,469 + -1.8
86,869 + -1.8
86,871 + -4.0
86,987 + -1.3
86,988 - -3.8
86,988 - -0.8
86,988 - -3.3
87,094 - HMPREF1058_RS01585 0.15 -2.9
87,094 - HMPREF1058_RS01585 0.15 -1.8
87,229 + HMPREF1058_RS01585 0.24 -0.8
87,236 - HMPREF1058_RS01585 0.25 -2.6
87,437 + HMPREF1058_RS01585 0.39 -2.0
87,438 - HMPREF1058_RS01585 0.39 +1.2
87,500 + HMPREF1058_RS01585 0.43 -1.3
87,500 + HMPREF1058_RS01585 0.43 -1.3
87,501 - HMPREF1058_RS01585 0.43 -2.3
87,707 + HMPREF1058_RS01585 0.57 -1.8
87,767 + HMPREF1058_RS01585 0.61 -3.6
87,825 - HMPREF1058_RS01585 0.65 -0.6
87,832 + HMPREF1058_RS01585 0.66 -0.6
87,977 + HMPREF1058_RS01585 0.76 -0.4
87,977 + HMPREF1058_RS01585 0.76 -0.8
88,010 + HMPREF1058_RS01585 0.78 -4.0
88,077 - HMPREF1058_RS01585 0.83 -2.2
88,257 + -2.8
88,277 - -1.3
88,292 - +0.2
88,313 - -1.6
88,374 + +1.5
88,403 - +0.2
88,412 - -1.3
88,473 + HMPREF1058_RS01580 0.12 +0.7
88,473 + HMPREF1058_RS01580 0.12 -0.5
88,474 - HMPREF1058_RS01580 0.12 -1.2
88,497 + HMPREF1058_RS01580 0.18 +0.4
88,498 - HMPREF1058_RS01580 0.18 +2.7
88,526 - HMPREF1058_RS01580 0.25 -2.8
88,578 - HMPREF1058_RS01580 0.37 -1.3
88,588 + HMPREF1058_RS01580 0.40 -0.8
88,594 - HMPREF1058_RS01580 0.41 -1.3
88,620 + HMPREF1058_RS01580 0.48 -2.3
88,866 - +0.7
88,966 - HMPREF1058_RS01575 0.23 -1.3
88,966 - HMPREF1058_RS01575 0.23 -2.1
88,976 + HMPREF1058_RS01575 0.24 +0.2
88,976 + HMPREF1058_RS01575 0.24 -2.6
88,976 + HMPREF1058_RS01575 0.24 +0.2
89,031 + HMPREF1058_RS01575 0.32 -0.0
89,031 + HMPREF1058_RS01575 0.32 -2.6
89,032 - HMPREF1058_RS01575 0.32 +0.4
89,054 - HMPREF1058_RS01575 0.35 -1.3
89,103 - HMPREF1058_RS01575 0.42 -0.6
89,189 + HMPREF1058_RS01575 0.53 -0.8
89,190 - HMPREF1058_RS01575 0.54 -2.7
89,194 - HMPREF1058_RS01575 0.54 -1.3
89,194 - HMPREF1058_RS01575 0.54 -1.8

Or see this region's nucleotide sequence