Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS16935

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_RS16945 and HMPREF1058_RS16940 are separated by 44 nucleotidesHMPREF1058_RS16940 and HMPREF1058_RS16935 are separated by 11 nucleotidesHMPREF1058_RS16935 and HMPREF1058_RS16930 are separated by 273 nucleotides HMPREF1058_RS16945: HMPREF1058_RS16945 - RNA polymerase sigma factor, at 554,435 to 554,986 _RS16945 HMPREF1058_RS16940: HMPREF1058_RS16940 - hypothetical protein, at 555,031 to 555,408 _RS16940 HMPREF1058_RS16935: HMPREF1058_RS16935 - hypothetical protein, at 555,420 to 555,866 _RS16935 HMPREF1058_RS16930: HMPREF1058_RS16930 - TonB-dependent receptor, at 556,140 to 559,301 _RS16930 Position (kb) 555 556Strain fitness (log2 ratio) -5 -4 -3 -2 -1 0 1 2at 554.445 kb on - strandat 554.461 kb on - strandat 554.535 kb on + strand, within HMPREF1058_RS16945at 554.535 kb on + strand, within HMPREF1058_RS16945at 554.535 kb on + strand, within HMPREF1058_RS16945at 554.548 kb on - strand, within HMPREF1058_RS16945at 554.548 kb on - strand, within HMPREF1058_RS16945at 554.623 kb on - strand, within HMPREF1058_RS16945at 554.670 kb on + strand, within HMPREF1058_RS16945at 554.777 kb on + strand, within HMPREF1058_RS16945at 554.777 kb on + strand, within HMPREF1058_RS16945at 554.845 kb on + strand, within HMPREF1058_RS16945at 554.846 kb on - strand, within HMPREF1058_RS16945at 554.847 kb on + strand, within HMPREF1058_RS16945at 554.848 kb on - strand, within HMPREF1058_RS16945at 554.865 kb on - strand, within HMPREF1058_RS16945at 554.883 kb on - strand, within HMPREF1058_RS16945at 554.914 kb on + strand, within HMPREF1058_RS16945at 555.129 kb on + strand, within HMPREF1058_RS16940at 555.130 kb on - strand, within HMPREF1058_RS16940at 555.173 kb on + strand, within HMPREF1058_RS16940at 555.178 kb on - strand, within HMPREF1058_RS16940at 555.190 kb on - strand, within HMPREF1058_RS16940at 555.205 kb on + strand, within HMPREF1058_RS16940at 555.205 kb on + strand, within HMPREF1058_RS16940at 555.205 kb on + strand, within HMPREF1058_RS16940at 555.206 kb on - strand, within HMPREF1058_RS16940at 555.206 kb on - strand, within HMPREF1058_RS16940at 555.207 kb on + strand, within HMPREF1058_RS16940at 555.207 kb on + strand, within HMPREF1058_RS16940at 555.207 kb on + strand, within HMPREF1058_RS16940at 555.208 kb on - strand, within HMPREF1058_RS16940at 555.208 kb on - strand, within HMPREF1058_RS16940at 555.208 kb on - strand, within HMPREF1058_RS16940at 555.216 kb on + strand, within HMPREF1058_RS16940at 555.254 kb on + strand, within HMPREF1058_RS16940at 555.254 kb on + strand, within HMPREF1058_RS16940at 555.254 kb on + strand, within HMPREF1058_RS16940at 555.255 kb on - strand, within HMPREF1058_RS16940at 555.255 kb on - strand, within HMPREF1058_RS16940at 555.255 kb on - strandat 555.319 kb on + strand, within HMPREF1058_RS16940at 555.320 kb on - strand, within HMPREF1058_RS16940at 555.321 kb on + strand, within HMPREF1058_RS16940at 555.360 kb on + strand, within HMPREF1058_RS16940at 555.396 kb on + strandat 555.401 kb on - strandat 555.424 kb on + strandat 555.425 kb on - strandat 555.425 kb on - strandat 555.454 kb on + strandat 555.455 kb on - strandat 555.456 kb on + strandat 555.457 kb on - strandat 555.458 kb on + strandat 555.458 kb on + strandat 555.537 kb on + strand, within HMPREF1058_RS16935at 555.537 kb on + strand, within HMPREF1058_RS16935at 555.538 kb on - strand, within HMPREF1058_RS16935at 555.698 kb on + strand, within HMPREF1058_RS16935at 555.699 kb on - strand, within HMPREF1058_RS16935at 555.700 kb on + strand, within HMPREF1058_RS16935at 555.701 kb on + strand, within HMPREF1058_RS16935at 555.701 kb on - strand, within HMPREF1058_RS16935at 555.708 kb on - strand, within HMPREF1058_RS16935at 555.708 kb on - strand, within HMPREF1058_RS16935at 555.750 kb on + strand, within HMPREF1058_RS16935at 555.754 kb on + strand, within HMPREF1058_RS16935at 555.754 kb on + strand, within HMPREF1058_RS16935at 555.755 kb on - strand, within HMPREF1058_RS16935at 555.795 kb on - strand, within HMPREF1058_RS16935at 555.904 kb on + strandat 556.090 kb on + strandat 556.128 kb on - strandat 556.153 kb on + strandat 556.153 kb on + strandat 556.156 kb on + strandat 556.159 kb on + strandat 556.169 kb on - strandat 556.174 kb on + strandat 556.175 kb on - strandat 556.186 kb on + strandat 556.187 kb on - strandat 556.274 kb on - strandat 556.326 kb on - strandat 556.539 kb on - strand, within HMPREF1058_RS16930at 556.642 kb on + strand, within HMPREF1058_RS16930at 556.643 kb on - strand, within HMPREF1058_RS16930at 556.732 kb on + strand, within HMPREF1058_RS16930at 556.732 kb on + strand, within HMPREF1058_RS16930at 556.733 kb on - strand, within HMPREF1058_RS16930at 556.733 kb on - strand, within HMPREF1058_RS16930at 556.774 kb on + strand, within HMPREF1058_RS16930at 556.774 kb on + strand, within HMPREF1058_RS16930at 556.774 kb on + strand, within HMPREF1058_RS16930at 556.774 kb on + strand, within HMPREF1058_RS16930at 556.775 kb on - strand, within HMPREF1058_RS16930at 556.775 kb on - strand, within HMPREF1058_RS16930at 556.775 kb on - strand, within HMPREF1058_RS16930at 556.775 kb on - strand, within HMPREF1058_RS16930at 556.775 kb on - strand, within HMPREF1058_RS16930at 556.777 kb on - strand, within HMPREF1058_RS16930at 556.830 kb on - strand, within HMPREF1058_RS16930at 556.852 kb on + strand, within HMPREF1058_RS16930

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse7; day4
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554,445 - -2.7
554,461 - +1.2
554,535 + HMPREF1058_RS16945 0.18 +1.2
554,535 + HMPREF1058_RS16945 0.18 -2.4
554,535 + HMPREF1058_RS16945 0.18 +1.2
554,548 - HMPREF1058_RS16945 0.20 -1.6
554,548 - HMPREF1058_RS16945 0.20 -1.0
554,623 - HMPREF1058_RS16945 0.34 +0.0
554,670 + HMPREF1058_RS16945 0.43 +2.4
554,777 + HMPREF1058_RS16945 0.62 -1.2
554,777 + HMPREF1058_RS16945 0.62 -0.4
554,845 + HMPREF1058_RS16945 0.74 +0.2
554,846 - HMPREF1058_RS16945 0.74 -0.9
554,847 + HMPREF1058_RS16945 0.75 +1.9
554,848 - HMPREF1058_RS16945 0.75 -2.0
554,865 - HMPREF1058_RS16945 0.78 -1.3
554,883 - HMPREF1058_RS16945 0.81 -1.3
554,914 + HMPREF1058_RS16945 0.87 +0.9
555,129 + HMPREF1058_RS16940 0.26 +0.8
555,130 - HMPREF1058_RS16940 0.26 -1.5
555,173 + HMPREF1058_RS16940 0.38 -1.6
555,178 - HMPREF1058_RS16940 0.39 +0.6
555,190 - HMPREF1058_RS16940 0.42 +0.0
555,205 + HMPREF1058_RS16940 0.46 +0.0
555,205 + HMPREF1058_RS16940 0.46 +0.6
555,205 + HMPREF1058_RS16940 0.46 -1.0
555,206 - HMPREF1058_RS16940 0.46 +2.6
555,206 - HMPREF1058_RS16940 0.46 +0.2
555,207 + HMPREF1058_RS16940 0.47 +0.6
555,207 + HMPREF1058_RS16940 0.47 -0.6
555,207 + HMPREF1058_RS16940 0.47 +0.4
555,208 - HMPREF1058_RS16940 0.47 -1.1
555,208 - HMPREF1058_RS16940 0.47 -3.0
555,208 - HMPREF1058_RS16940 0.47 +0.0
555,216 + HMPREF1058_RS16940 0.49 -1.0
555,254 + HMPREF1058_RS16940 0.59 -1.0
555,254 + HMPREF1058_RS16940 0.59 -1.9
555,254 + HMPREF1058_RS16940 0.59 -0.4
555,255 - HMPREF1058_RS16940 0.59 -2.1
555,255 - HMPREF1058_RS16940 0.59 -1.0
555,255 - -1.0
555,319 + HMPREF1058_RS16940 0.76 -3.3
555,320 - HMPREF1058_RS16940 0.76 -3.0
555,321 + HMPREF1058_RS16940 0.77 -2.6
555,360 + HMPREF1058_RS16940 0.87 -3.2
555,396 + +1.8
555,401 - -1.9
555,424 + -1.0
555,425 - -3.0
555,425 - -1.3
555,454 + -4.4
555,455 - -2.3
555,456 + -4.8
555,457 - -2.7
555,458 + -3.6
555,458 + -2.0
555,537 + HMPREF1058_RS16935 0.26 -2.8
555,537 + HMPREF1058_RS16935 0.26 -3.5
555,538 - HMPREF1058_RS16935 0.26 +0.0
555,698 + HMPREF1058_RS16935 0.62 -2.3
555,699 - HMPREF1058_RS16935 0.62 -2.6
555,700 + HMPREF1058_RS16935 0.63 -3.7
555,701 + HMPREF1058_RS16935 0.63 -5.4
555,701 - HMPREF1058_RS16935 0.63 -2.8
555,708 - HMPREF1058_RS16935 0.64 -0.6
555,708 - HMPREF1058_RS16935 0.64 -2.8
555,750 + HMPREF1058_RS16935 0.74 -4.2
555,754 + HMPREF1058_RS16935 0.75 -1.0
555,754 + HMPREF1058_RS16935 0.75 -3.1
555,755 - HMPREF1058_RS16935 0.75 +0.0
555,795 - HMPREF1058_RS16935 0.84 -3.0
555,904 + +0.2
556,090 + -0.6
556,128 - +1.0
556,153 + -1.7
556,153 + +0.0
556,156 + +0.3
556,159 + +2.0
556,169 - +2.3
556,174 + -1.2
556,175 - +0.4
556,186 + -2.0
556,187 - +0.0
556,274 - +0.7
556,326 - +2.0
556,539 - HMPREF1058_RS16930 0.13 +0.0
556,642 + HMPREF1058_RS16930 0.16 +0.9
556,643 - HMPREF1058_RS16930 0.16 +0.2
556,732 + HMPREF1058_RS16930 0.19 -1.2
556,732 + HMPREF1058_RS16930 0.19 +0.9
556,733 - HMPREF1058_RS16930 0.19 +1.0
556,733 - HMPREF1058_RS16930 0.19 +0.1
556,774 + HMPREF1058_RS16930 0.20 +0.9
556,774 + HMPREF1058_RS16930 0.20 -1.0
556,774 + HMPREF1058_RS16930 0.20 +0.7
556,774 + HMPREF1058_RS16930 0.20 +0.0
556,775 - HMPREF1058_RS16930 0.20 +1.3
556,775 - HMPREF1058_RS16930 0.20 +0.3
556,775 - HMPREF1058_RS16930 0.20 +1.5
556,775 - HMPREF1058_RS16930 0.20 +1.0
556,775 - HMPREF1058_RS16930 0.20 -1.9
556,777 - HMPREF1058_RS16930 0.20 -0.7
556,830 - HMPREF1058_RS16930 0.22 +0.9
556,852 + HMPREF1058_RS16930 0.23 -0.3

Or see this region's nucleotide sequence