Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS01520

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day2

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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_RS01525 and HMPREF1058_RS01520 are separated by 31 nucleotidesHMPREF1058_RS01520 and HMPREF1058_RS01515 are separated by 186 nucleotides HMPREF1058_RS01525: HMPREF1058_RS01525 - helix-turn-helix transcriptional regulator, at 101,230 to 102,138 _RS01525 HMPREF1058_RS01520: HMPREF1058_RS01520 - helix-turn-helix transcriptional regulator, at 102,170 to 103,057 _RS01520 HMPREF1058_RS01515: HMPREF1058_RS01515 - 1-deoxy-D-xylulose-5-phosphate synthase, at 103,244 to 105,004 _RS01515 Position (kb) 102 103 104Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3 4at 101.214 kb on + strandat 101.240 kb on + strandat 101.268 kb on + strandat 101.269 kb on - strandat 101.348 kb on - strand, within HMPREF1058_RS01525at 101.348 kb on - strand, within HMPREF1058_RS01525at 101.413 kb on + strand, within HMPREF1058_RS01525at 101.414 kb on - strand, within HMPREF1058_RS01525at 101.643 kb on + strand, within HMPREF1058_RS01525at 101.643 kb on + strand, within HMPREF1058_RS01525at 101.643 kb on + strand, within HMPREF1058_RS01525at 101.700 kb on + strand, within HMPREF1058_RS01525at 101.701 kb on - strand, within HMPREF1058_RS01525at 101.703 kb on + strand, within HMPREF1058_RS01525at 101.722 kb on + strand, within HMPREF1058_RS01525at 101.723 kb on - strand, within HMPREF1058_RS01525at 101.723 kb on - strand, within HMPREF1058_RS01525at 101.726 kb on + strand, within HMPREF1058_RS01525at 101.727 kb on - strand, within HMPREF1058_RS01525at 101.727 kb on - strand, within HMPREF1058_RS01525at 101.759 kb on - strand, within HMPREF1058_RS01525at 101.925 kb on + strand, within HMPREF1058_RS01525at 101.963 kb on - strand, within HMPREF1058_RS01525at 101.963 kb on - strand, within HMPREF1058_RS01525at 101.964 kb on + strand, within HMPREF1058_RS01525at 102.134 kb on + strandat 102.134 kb on + strandat 102.134 kb on + strandat 102.156 kb on + strandat 102.170 kb on - strandat 102.189 kb on + strandat 102.190 kb on - strandat 102.191 kb on + strandat 102.192 kb on - strandat 102.296 kb on + strand, within HMPREF1058_RS01520at 102.296 kb on + strand, within HMPREF1058_RS01520at 102.297 kb on - strand, within HMPREF1058_RS01520at 102.356 kb on + strand, within HMPREF1058_RS01520at 102.357 kb on - strand, within HMPREF1058_RS01520at 102.357 kb on - strand, within HMPREF1058_RS01520at 102.424 kb on + strand, within HMPREF1058_RS01520at 102.509 kb on - strand, within HMPREF1058_RS01520at 102.591 kb on + strand, within HMPREF1058_RS01520at 102.592 kb on - strand, within HMPREF1058_RS01520at 102.625 kb on + strand, within HMPREF1058_RS01520at 102.626 kb on - strand, within HMPREF1058_RS01520at 102.626 kb on - strand, within HMPREF1058_RS01520at 102.631 kb on + strand, within HMPREF1058_RS01520at 102.635 kb on - strand, within HMPREF1058_RS01520at 102.652 kb on - strand, within HMPREF1058_RS01520at 102.759 kb on - strand, within HMPREF1058_RS01520at 102.760 kb on + strand, within HMPREF1058_RS01520at 102.808 kb on + strand, within HMPREF1058_RS01520at 103.129 kb on + strandat 103.134 kb on - strandat 103.247 kb on + strandat 103.248 kb on - strandat 103.303 kb on - strandat 103.401 kb on + strandat 103.412 kb on + strandat 103.443 kb on + strand, within HMPREF1058_RS01515at 103.443 kb on + strand, within HMPREF1058_RS01515at 103.444 kb on - strand, within HMPREF1058_RS01515at 103.444 kb on - strand, within HMPREF1058_RS01515at 103.445 kb on + strand, within HMPREF1058_RS01515at 103.445 kb on + strand, within HMPREF1058_RS01515at 103.446 kb on - strand, within HMPREF1058_RS01515at 103.453 kb on - strand, within HMPREF1058_RS01515at 103.466 kb on + strand, within HMPREF1058_RS01515at 103.469 kb on - strand, within HMPREF1058_RS01515at 103.521 kb on - strand, within HMPREF1058_RS01515at 103.744 kb on + strand, within HMPREF1058_RS01515at 103.745 kb on - strand, within HMPREF1058_RS01515at 103.746 kb on + strand, within HMPREF1058_RS01515at 103.747 kb on - strand, within HMPREF1058_RS01515at 103.877 kb on + strand, within HMPREF1058_RS01515at 103.878 kb on - strand, within HMPREF1058_RS01515at 103.936 kb on + strand, within HMPREF1058_RS01515at 103.936 kb on + strand, within HMPREF1058_RS01515at 103.937 kb on - strand, within HMPREF1058_RS01515at 103.937 kb on - strand, within HMPREF1058_RS01515

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day2
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101,214 + -2.0
101,240 + -1.0
101,268 + +1.3
101,269 - +0.8
101,348 - HMPREF1058_RS01525 0.13 +0.7
101,348 - HMPREF1058_RS01525 0.13 +1.9
101,413 + HMPREF1058_RS01525 0.20 -2.2
101,414 - HMPREF1058_RS01525 0.20 -0.4
101,643 + HMPREF1058_RS01525 0.45 -2.4
101,643 + HMPREF1058_RS01525 0.45 +0.8
101,643 + HMPREF1058_RS01525 0.45 -1.0
101,700 + HMPREF1058_RS01525 0.52 +0.8
101,701 - HMPREF1058_RS01525 0.52 -1.0
101,703 + HMPREF1058_RS01525 0.52 -0.4
101,722 + HMPREF1058_RS01525 0.54 +0.8
101,723 - HMPREF1058_RS01525 0.54 -1.4
101,723 - HMPREF1058_RS01525 0.54 +1.6
101,726 + HMPREF1058_RS01525 0.55 +2.5
101,727 - HMPREF1058_RS01525 0.55 -2.0
101,727 - HMPREF1058_RS01525 0.55 +2.2
101,759 - HMPREF1058_RS01525 0.58 +0.6
101,925 + HMPREF1058_RS01525 0.76 -0.5
101,963 - HMPREF1058_RS01525 0.81 +0.8
101,963 - HMPREF1058_RS01525 0.81 -2.0
101,964 + HMPREF1058_RS01525 0.81 +0.5
102,134 + +1.0
102,134 + +0.9
102,134 + -0.4
102,156 + +0.6
102,170 - +1.5
102,189 + +0.6
102,190 - -0.4
102,191 + -0.4
102,192 - +0.9
102,296 + HMPREF1058_RS01520 0.14 +0.0
102,296 + HMPREF1058_RS01520 0.14 -1.4
102,297 - HMPREF1058_RS01520 0.14 -0.5
102,356 + HMPREF1058_RS01520 0.21 -0.4
102,357 - HMPREF1058_RS01520 0.21 -1.4
102,357 - HMPREF1058_RS01520 0.21 +2.2
102,424 + HMPREF1058_RS01520 0.29 -1.4
102,509 - HMPREF1058_RS01520 0.38 -3.4
102,591 + HMPREF1058_RS01520 0.47 -2.4
102,592 - HMPREF1058_RS01520 0.48 +2.8
102,625 + HMPREF1058_RS01520 0.51 +0.6
102,626 - HMPREF1058_RS01520 0.51 +1.4
102,626 - HMPREF1058_RS01520 0.51 -1.4
102,631 + HMPREF1058_RS01520 0.52 +3.1
102,635 - HMPREF1058_RS01520 0.52 +2.2
102,652 - HMPREF1058_RS01520 0.54 +1.8
102,759 - HMPREF1058_RS01520 0.66 -0.5
102,760 + HMPREF1058_RS01520 0.66 +0.4
102,808 + HMPREF1058_RS01520 0.72 +1.0
103,129 + +0.9
103,134 - +4.7
103,247 + +1.4
103,248 - -1.0
103,303 - -1.7
103,401 + +1.4
103,412 + +1.2
103,443 + HMPREF1058_RS01515 0.11 -1.7
103,443 + HMPREF1058_RS01515 0.11 +2.6
103,444 - HMPREF1058_RS01515 0.11 -1.4
103,444 - HMPREF1058_RS01515 0.11 -1.7
103,445 + HMPREF1058_RS01515 0.11 +1.8
103,445 + HMPREF1058_RS01515 0.11 -2.0
103,446 - HMPREF1058_RS01515 0.11 -1.4
103,453 - HMPREF1058_RS01515 0.12 -2.0
103,466 + HMPREF1058_RS01515 0.13 -0.4
103,469 - HMPREF1058_RS01515 0.13 -1.7
103,521 - HMPREF1058_RS01515 0.16 +1.8
103,744 + HMPREF1058_RS01515 0.28 +0.0
103,745 - HMPREF1058_RS01515 0.28 +1.8
103,746 + HMPREF1058_RS01515 0.29 -1.7
103,747 - HMPREF1058_RS01515 0.29 -1.4
103,877 + HMPREF1058_RS01515 0.36 +0.6
103,878 - HMPREF1058_RS01515 0.36 +1.8
103,936 + HMPREF1058_RS01515 0.39 -0.4
103,936 + HMPREF1058_RS01515 0.39 +0.6
103,937 - HMPREF1058_RS01515 0.39 -3.2
103,937 - HMPREF1058_RS01515 0.39 -0.4

Or see this region's nucleotide sequence