Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS04235

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_RS04240 and HMPREF1058_RS04235 are separated by 205 nucleotidesHMPREF1058_RS04235 and HMPREF1058_RS04230 are separated by 387 nucleotidesHMPREF1058_RS04230 and HMPREF1058_RS04225 are separated by 91 nucleotides HMPREF1058_RS04240: HMPREF1058_RS04240 - DUF5131 family protein, at 84,832 to 85,599 _RS04240 HMPREF1058_RS04235: HMPREF1058_RS04235 - NUDIX hydrolase, at 85,805 to 86,359 _RS04235 HMPREF1058_RS04230: HMPREF1058_RS04230 - pyridoxamine 5'-phosphate oxidase family protein, at 86,747 to 87,166 _RS04230 HMPREF1058_RS04225: HMPREF1058_RS04225 - helix-turn-helix transcriptional regulator, at 87,258 to 88,148 _RS04225 Position (kb) 85 86 87Strain fitness (log2 ratio) -3 -2 -1 0 1at 84.842 kb on + strandat 84.847 kb on - strandat 84.847 kb on - strandat 84.875 kb on - strandat 84.897 kb on + strandat 84.917 kb on - strand, within HMPREF1058_RS04240at 84.941 kb on - strand, within HMPREF1058_RS04240at 84.976 kb on + strand, within HMPREF1058_RS04240at 84.976 kb on + strand, within HMPREF1058_RS04240at 84.977 kb on - strand, within HMPREF1058_RS04240at 84.991 kb on - strand, within HMPREF1058_RS04240at 85.026 kb on + strand, within HMPREF1058_RS04240at 85.030 kb on + strand, within HMPREF1058_RS04240at 85.030 kb on + strand, within HMPREF1058_RS04240at 85.030 kb on + strand, within HMPREF1058_RS04240at 85.031 kb on - strand, within HMPREF1058_RS04240at 85.032 kb on + strand, within HMPREF1058_RS04240at 85.032 kb on + strand, within HMPREF1058_RS04240at 85.083 kb on + strand, within HMPREF1058_RS04240at 85.106 kb on - strandat 85.106 kb on - strand, within HMPREF1058_RS04240at 85.225 kb on - strand, within HMPREF1058_RS04240at 85.274 kb on - strand, within HMPREF1058_RS04240at 85.336 kb on + strand, within HMPREF1058_RS04240at 85.336 kb on + strand, within HMPREF1058_RS04240at 85.389 kb on - strand, within HMPREF1058_RS04240at 85.389 kb on - strand, within HMPREF1058_RS04240at 85.415 kb on + strand, within HMPREF1058_RS04240at 85.494 kb on + strand, within HMPREF1058_RS04240at 85.510 kb on + strand, within HMPREF1058_RS04240at 85.510 kb on + strand, within HMPREF1058_RS04240at 85.510 kb on - strand, within HMPREF1058_RS04240at 85.511 kb on - strand, within HMPREF1058_RS04240at 85.514 kb on + strand, within HMPREF1058_RS04240at 85.514 kb on + strand, within HMPREF1058_RS04240at 85.515 kb on - strand, within HMPREF1058_RS04240at 85.537 kb on + strandat 85.586 kb on - strandat 85.586 kb on - strandat 85.611 kb on - strandat 85.635 kb on + strandat 85.635 kb on + strandat 85.658 kb on - strandat 85.661 kb on + strandat 85.702 kb on + strandat 85.726 kb on - strandat 85.739 kb on + strandat 85.764 kb on + strandat 85.771 kb on + strandat 85.772 kb on - strandat 85.773 kb on + strandat 85.778 kb on + strandat 85.779 kb on - strandat 85.779 kb on - strandat 85.786 kb on - strandat 85.802 kb on + strandat 85.805 kb on - strandat 85.847 kb on + strandat 85.847 kb on + strandat 85.896 kb on + strand, within HMPREF1058_RS04235at 85.896 kb on + strand, within HMPREF1058_RS04235at 85.925 kb on + strand, within HMPREF1058_RS04235at 85.927 kb on + strand, within HMPREF1058_RS04235at 85.951 kb on - strand, within HMPREF1058_RS04235at 85.956 kb on + strand, within HMPREF1058_RS04235at 85.990 kb on - strand, within HMPREF1058_RS04235at 86.346 kb on - strandat 86.357 kb on + strandat 86.358 kb on - strandat 86.358 kb on - strandat 86.360 kb on + strandat 86.366 kb on + strandat 86.366 kb on + strandat 86.367 kb on - strandat 86.367 kb on - strandat 86.367 kb on - strandat 86.367 kb on - strandat 86.368 kb on + strandat 86.368 kb on + strandat 86.368 kb on + strandat 86.369 kb on - strandat 86.410 kb on + strandat 86.459 kb on - strandat 86.472 kb on + strandat 86.816 kb on + strand, within HMPREF1058_RS04230at 86.823 kb on + strand, within HMPREF1058_RS04230at 86.853 kb on + strand, within HMPREF1058_RS04230at 86.993 kb on + strand, within HMPREF1058_RS04230at 86.994 kb on - strand, within HMPREF1058_RS04230at 87.052 kb on + strand, within HMPREF1058_RS04230at 87.053 kb on - strand, within HMPREF1058_RS04230at 87.080 kb on - strand, within HMPREF1058_RS04230at 87.232 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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84,842 + -0.6
84,847 - -0.3
84,847 - +0.1
84,875 - +1.7
84,897 + -1.3
84,917 - HMPREF1058_RS04240 0.11 -0.5
84,941 - HMPREF1058_RS04240 0.14 +1.0
84,976 + HMPREF1058_RS04240 0.19 -2.3
84,976 + HMPREF1058_RS04240 0.19 +0.4
84,977 - HMPREF1058_RS04240 0.19 +0.7
84,991 - HMPREF1058_RS04240 0.21 +0.7
85,026 + HMPREF1058_RS04240 0.25 -1.3
85,030 + HMPREF1058_RS04240 0.26 -0.5
85,030 + HMPREF1058_RS04240 0.26 -0.6
85,030 + HMPREF1058_RS04240 0.26 -0.5
85,031 - HMPREF1058_RS04240 0.26 -2.9
85,032 + HMPREF1058_RS04240 0.26 -0.3
85,032 + HMPREF1058_RS04240 0.26 +0.8
85,083 + HMPREF1058_RS04240 0.33 -0.7
85,106 - +0.9
85,106 - HMPREF1058_RS04240 0.36 +0.3
85,225 - HMPREF1058_RS04240 0.51 +0.3
85,274 - HMPREF1058_RS04240 0.58 +0.1
85,336 + HMPREF1058_RS04240 0.66 -0.6
85,336 + HMPREF1058_RS04240 0.66 +0.5
85,389 - HMPREF1058_RS04240 0.73 +0.4
85,389 - HMPREF1058_RS04240 0.73 +1.6
85,415 + HMPREF1058_RS04240 0.76 +0.4
85,494 + HMPREF1058_RS04240 0.86 -0.8
85,510 + HMPREF1058_RS04240 0.88 -1.2
85,510 + HMPREF1058_RS04240 0.88 -0.1
85,510 - HMPREF1058_RS04240 0.88 -1.1
85,511 - HMPREF1058_RS04240 0.88 -0.5
85,514 + HMPREF1058_RS04240 0.89 -0.5
85,514 + HMPREF1058_RS04240 0.89 +0.4
85,515 - HMPREF1058_RS04240 0.89 +0.5
85,537 + -1.6
85,586 - -0.0
85,586 - -0.2
85,611 - +0.9
85,635 + -0.1
85,635 + -0.3
85,658 - +0.1
85,661 + -0.8
85,702 + -0.2
85,726 - -0.6
85,739 + -0.1
85,764 + -1.5
85,771 + +0.3
85,772 - -0.4
85,773 + +1.5
85,778 + +0.0
85,779 - -1.1
85,779 - +0.6
85,786 - +0.1
85,802 + +0.4
85,805 - -1.3
85,847 + +0.1
85,847 + -1.6
85,896 + HMPREF1058_RS04235 0.16 +0.1
85,896 + HMPREF1058_RS04235 0.16 +0.0
85,925 + HMPREF1058_RS04235 0.22 +1.0
85,927 + HMPREF1058_RS04235 0.22 +0.8
85,951 - HMPREF1058_RS04235 0.26 -0.3
85,956 + HMPREF1058_RS04235 0.27 +1.4
85,990 - HMPREF1058_RS04235 0.33 +0.5
86,346 - -0.6
86,357 + +0.4
86,358 - +0.6
86,358 - +0.2
86,360 + -0.2
86,366 + -0.3
86,366 + +0.3
86,367 - -0.3
86,367 - -0.2
86,367 - +0.3
86,367 - +0.6
86,368 + +0.8
86,368 + -0.2
86,368 + +0.1
86,369 - -1.7
86,410 + -0.0
86,459 - -0.1
86,472 + -0.5
86,816 + HMPREF1058_RS04230 0.16 +0.5
86,823 + HMPREF1058_RS04230 0.18 -0.1
86,853 + HMPREF1058_RS04230 0.25 +0.3
86,993 + HMPREF1058_RS04230 0.59 +1.0
86,994 - HMPREF1058_RS04230 0.59 +0.4
87,052 + HMPREF1058_RS04230 0.73 +0.1
87,053 - HMPREF1058_RS04230 0.73 -1.0
87,080 - HMPREF1058_RS04230 0.79 -1.2
87,232 - -0.4

Or see this region's nucleotide sequence