Strain Fitness in Parabacteroides merdae CL09T00C40 around HMPREF1078_RS04780

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; 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 ntHMPREF1078_RS04765 and HMPREF1078_RS04770 overlap by 8 nucleotidesHMPREF1078_RS04770 and HMPREF1078_RS04775 are separated by 14 nucleotidesHMPREF1078_RS04775 and HMPREF1078_RS04780 are separated by 69 nucleotidesHMPREF1078_RS04780 and HMPREF1078_RS04785 overlap by 4 nucleotidesHMPREF1078_RS04785 and HMPREF1078_RS04790 are separated by 5 nucleotidesHMPREF1078_RS04790 and HMPREF1078_RS04795 are separated by 52 nucleotides HMPREF1078_RS04765: HMPREF1078_RS04765 - biotin--[acetyl-CoA-carboxylase] ligase, at 204,789 to 205,544 _RS04765 HMPREF1078_RS04770: HMPREF1078_RS04770 - MmcQ/YjbR family DNA-binding protein, at 205,537 to 205,893 _RS04770 HMPREF1078_RS04775: HMPREF1078_RS04775 - YraN family protein, at 205,908 to 206,276 _RS04775 HMPREF1078_RS04780: HMPREF1078_RS04780 - hypothetical protein, at 206,346 to 206,573 _RS04780 HMPREF1078_RS04785: HMPREF1078_RS04785 - nucleoside deaminase, at 206,570 to 207,013 _RS04785 HMPREF1078_RS04790: HMPREF1078_RS04790 - DUF4834 family protein, at 207,019 to 207,285 _RS04790 HMPREF1078_RS04795: HMPREF1078_RS04795 - CDP-alcohol phosphatidyltransferase family protein, at 207,338 to 208,042 _RS04795 Position (kb) 206 207Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2 3at 205.650 kb on - strand, within HMPREF1078_RS04770at 205.702 kb on - strand, within HMPREF1078_RS04770at 205.702 kb on - strand, within HMPREF1078_RS04770at 205.728 kb on - strand, within HMPREF1078_RS04770at 205.886 kb on - strandat 205.888 kb on - strandat 205.942 kb on - strandat 206.030 kb on - strand, within HMPREF1078_RS04775at 206.052 kb on - strand, within HMPREF1078_RS04775at 206.142 kb on - strand, within HMPREF1078_RS04775at 206.171 kb on - strand, within HMPREF1078_RS04775at 206.297 kb on - strandat 206.297 kb on - strandat 206.297 kb on - strandat 206.299 kb on - strandat 206.333 kb on - strandat 206.360 kb on + strandat 206.360 kb on + strandat 206.365 kb on - strandat 206.448 kb on + strand, within HMPREF1078_RS04780at 206.449 kb on - strand, within HMPREF1078_RS04780at 206.460 kb on + strand, within HMPREF1078_RS04780at 206.463 kb on - strand, within HMPREF1078_RS04780at 206.512 kb on + strand, within HMPREF1078_RS04780at 206.512 kb on + strand, within HMPREF1078_RS04780at 206.513 kb on - strand, within HMPREF1078_RS04780at 206.513 kb on - strand, within HMPREF1078_RS04780at 206.516 kb on + strand, within HMPREF1078_RS04780at 206.516 kb on + strand, within HMPREF1078_RS04780at 206.516 kb on + strand, within HMPREF1078_RS04780at 206.517 kb on - strand, within HMPREF1078_RS04780at 206.535 kb on + strand, within HMPREF1078_RS04780at 206.540 kb on + strand, within HMPREF1078_RS04780at 206.541 kb on - strand, within HMPREF1078_RS04780at 206.613 kb on + strandat 206.614 kb on - strandat 206.616 kb on + strand, within HMPREF1078_RS04785at 206.670 kb on + strand, within HMPREF1078_RS04785at 206.670 kb on + strand, within HMPREF1078_RS04785at 206.670 kb on + strand, within HMPREF1078_RS04785at 206.674 kb on + strand, within HMPREF1078_RS04785at 206.674 kb on + strand, within HMPREF1078_RS04785at 206.675 kb on - strand, within HMPREF1078_RS04785at 206.675 kb on - strand, within HMPREF1078_RS04785at 206.677 kb on + strand, within HMPREF1078_RS04785at 206.677 kb on + strand, within HMPREF1078_RS04785at 206.748 kb on + strand, within HMPREF1078_RS04785at 206.749 kb on - strand, within HMPREF1078_RS04785at 206.786 kb on + strand, within HMPREF1078_RS04785at 206.786 kb on + strand, within HMPREF1078_RS04785at 206.786 kb on + strand, within HMPREF1078_RS04785at 206.808 kb on - strand, within HMPREF1078_RS04785at 206.808 kb on - strand, within HMPREF1078_RS04785at 206.862 kb on + strand, within HMPREF1078_RS04785at 206.877 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 206.929 kb on - strand, within HMPREF1078_RS04785at 207.020 kb on + strandat 207.021 kb on - strandat 207.036 kb on - strandat 207.044 kb on + strandat 207.044 kb on + strandat 207.045 kb on - strandat 207.075 kb on + strand, within HMPREF1078_RS04790at 207.095 kb on + strand, within HMPREF1078_RS04790at 207.095 kb on + strand, within HMPREF1078_RS04790at 207.096 kb on - strand, within HMPREF1078_RS04790at 207.096 kb on - strand, within HMPREF1078_RS04790at 207.137 kb on + strand, within HMPREF1078_RS04790at 207.137 kb on + strand, within HMPREF1078_RS04790at 207.205 kb on - strand, within HMPREF1078_RS04790at 207.210 kb on + strand, within HMPREF1078_RS04790at 207.211 kb on - strand, within HMPREF1078_RS04790at 207.219 kb on + strand, within HMPREF1078_RS04790at 207.219 kb on + strand, within HMPREF1078_RS04790at 207.220 kb on - strand, within HMPREF1078_RS04790at 207.220 kb on - strand, within HMPREF1078_RS04790at 207.280 kb on - strandat 207.307 kb on - strandat 207.325 kb on + strandat 207.339 kb on + strandat 207.340 kb on - strandat 207.340 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day4
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205,650 - HMPREF1078_RS04770 0.32 -0.9
205,702 - HMPREF1078_RS04770 0.46 +1.7
205,702 - HMPREF1078_RS04770 0.46 +0.5
205,728 - HMPREF1078_RS04770 0.54 -0.8
205,886 - -0.3
205,888 - +0.1
205,942 - -2.8
206,030 - HMPREF1078_RS04775 0.33 +0.4
206,052 - HMPREF1078_RS04775 0.39 +0.6
206,142 - HMPREF1078_RS04775 0.63 +0.1
206,171 - HMPREF1078_RS04775 0.71 -0.5
206,297 - +0.5
206,297 - -0.7
206,297 - -0.3
206,299 - -1.2
206,333 - -1.6
206,360 + +0.7
206,360 + +0.6
206,365 - -1.4
206,448 + HMPREF1078_RS04780 0.45 -1.3
206,449 - HMPREF1078_RS04780 0.45 -0.9
206,460 + HMPREF1078_RS04780 0.50 -0.0
206,463 - HMPREF1078_RS04780 0.51 -2.4
206,512 + HMPREF1078_RS04780 0.73 -0.4
206,512 + HMPREF1078_RS04780 0.73 -0.1
206,513 - HMPREF1078_RS04780 0.73 -1.7
206,513 - HMPREF1078_RS04780 0.73 -2.3
206,516 + HMPREF1078_RS04780 0.75 -1.4
206,516 + HMPREF1078_RS04780 0.75 -0.6
206,516 + HMPREF1078_RS04780 0.75 -1.9
206,517 - HMPREF1078_RS04780 0.75 -3.1
206,535 + HMPREF1078_RS04780 0.83 +0.8
206,540 + HMPREF1078_RS04780 0.85 +0.5
206,541 - HMPREF1078_RS04780 0.86 -1.9
206,613 + -1.6
206,614 - -3.4
206,616 + HMPREF1078_RS04785 0.10 -1.7
206,670 + HMPREF1078_RS04785 0.23 -2.6
206,670 + HMPREF1078_RS04785 0.23 -1.3
206,670 + HMPREF1078_RS04785 0.23 -1.3
206,674 + HMPREF1078_RS04785 0.23 -0.9
206,674 + HMPREF1078_RS04785 0.23 -1.1
206,675 - HMPREF1078_RS04785 0.24 -1.7
206,675 - HMPREF1078_RS04785 0.24 -1.7
206,677 + HMPREF1078_RS04785 0.24 -1.5
206,677 + HMPREF1078_RS04785 0.24 -1.9
206,748 + HMPREF1078_RS04785 0.40 -0.3
206,749 - HMPREF1078_RS04785 0.40 -2.8
206,786 + HMPREF1078_RS04785 0.49 -2.5
206,786 + HMPREF1078_RS04785 0.49 -4.6
206,786 + HMPREF1078_RS04785 0.49 -1.6
206,808 - HMPREF1078_RS04785 0.54 -3.0
206,808 - HMPREF1078_RS04785 0.54 -2.0
206,862 + HMPREF1078_RS04785 0.66 -0.7
206,877 - HMPREF1078_RS04785 0.69 -2.8
206,929 - HMPREF1078_RS04785 0.81 -3.4
206,929 - HMPREF1078_RS04785 0.81 -3.3
206,929 - HMPREF1078_RS04785 0.81 -2.6
206,929 - HMPREF1078_RS04785 0.81 -2.9
206,929 - HMPREF1078_RS04785 0.81 -1.6
206,929 - HMPREF1078_RS04785 0.81 -1.1
207,020 + +0.5
207,021 - -2.2
207,036 - -0.2
207,044 + -1.6
207,044 + +3.0
207,045 - -1.6
207,075 + HMPREF1078_RS04790 0.21 -2.2
207,095 + HMPREF1078_RS04790 0.28 -0.5
207,095 + HMPREF1078_RS04790 0.28 +1.0
207,096 - HMPREF1078_RS04790 0.29 -0.7
207,096 - HMPREF1078_RS04790 0.29 -1.0
207,137 + HMPREF1078_RS04790 0.44 -2.6
207,137 + HMPREF1078_RS04790 0.44 -0.5
207,205 - HMPREF1078_RS04790 0.70 -1.2
207,210 + HMPREF1078_RS04790 0.72 -1.6
207,211 - HMPREF1078_RS04790 0.72 -0.2
207,219 + HMPREF1078_RS04790 0.75 -3.4
207,219 + HMPREF1078_RS04790 0.75 -0.9
207,220 - HMPREF1078_RS04790 0.75 +1.2
207,220 - HMPREF1078_RS04790 0.75 +1.4
207,280 - -1.2
207,307 - +1.4
207,325 + -3.2
207,339 + -0.9
207,340 - -0.3
207,340 - -0.3

Or see this region's nucleotide sequence