Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS04375

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_RS04385 and HMPREF1058_RS04380 are separated by 93 nucleotidesHMPREF1058_RS04380 and HMPREF1058_RS04375 are separated by 114 nucleotidesHMPREF1058_RS04375 and HMPREF1058_RS04370 are separated by 11 nucleotides HMPREF1058_RS04385: HMPREF1058_RS04385 - methylated-DNA--[protein]-cysteine S-methyltransferase, at 47,647 to 48,174 _RS04385 HMPREF1058_RS04380: HMPREF1058_RS04380 - DUF4251 domain-containing protein, at 48,268 to 48,858 _RS04380 HMPREF1058_RS04375: HMPREF1058_RS04375 - carbon-nitrogen hydrolase, at 48,973 to 49,860 _RS04375 HMPREF1058_RS04370: HMPREF1058_RS04370 - agmatine deiminase family protein, at 49,872 to 50,903 _RS04370 Position (kb) 48 49 50Strain fitness (log2 ratio) -5 -4 -3 -2 -1 0 1 2at 47.975 kb on - strand, within HMPREF1058_RS04385at 48.170 kb on + strandat 48.170 kb on + strandat 48.199 kb on + strandat 48.200 kb on - strandat 48.202 kb on - strandat 48.207 kb on + strandat 48.254 kb on - strandat 48.261 kb on + strandat 48.270 kb on - strandat 48.290 kb on - strandat 48.294 kb on + strandat 48.294 kb on + strandat 48.336 kb on + strand, within HMPREF1058_RS04380at 48.359 kb on - strand, within HMPREF1058_RS04380at 48.361 kb on - strand, within HMPREF1058_RS04380at 48.361 kb on - strand, within HMPREF1058_RS04380at 48.361 kb on - strand, within HMPREF1058_RS04380at 48.364 kb on - strand, within HMPREF1058_RS04380at 48.441 kb on + strand, within HMPREF1058_RS04380at 48.442 kb on - strand, within HMPREF1058_RS04380at 48.443 kb on + strand, within HMPREF1058_RS04380at 48.479 kb on - strand, within HMPREF1058_RS04380at 48.479 kb on - strand, within HMPREF1058_RS04380at 48.535 kb on - strand, within HMPREF1058_RS04380at 48.594 kb on - strand, within HMPREF1058_RS04380at 48.638 kb on - strand, within HMPREF1058_RS04380at 48.638 kb on - strand, within HMPREF1058_RS04380at 48.677 kb on - strand, within HMPREF1058_RS04380at 48.685 kb on - strand, within HMPREF1058_RS04380at 48.685 kb on - strand, within HMPREF1058_RS04380at 48.699 kb on - strand, within HMPREF1058_RS04380at 48.700 kb on - strand, within HMPREF1058_RS04380at 48.827 kb on - strandat 48.874 kb on + strandat 48.885 kb on + strandat 48.886 kb on - strandat 48.909 kb on - strandat 48.970 kb on + strandat 49.086 kb on + strand, within HMPREF1058_RS04375at 49.121 kb on - strand, within HMPREF1058_RS04375at 49.276 kb on + strand, within HMPREF1058_RS04375at 49.322 kb on - strand, within HMPREF1058_RS04375at 49.322 kb on - strand, within HMPREF1058_RS04375at 49.324 kb on - strand, within HMPREF1058_RS04375at 49.330 kb on - strand, within HMPREF1058_RS04375at 49.335 kb on - strand, within HMPREF1058_RS04375at 49.335 kb on - strand, within HMPREF1058_RS04375at 49.337 kb on - strand, within HMPREF1058_RS04375at 49.337 kb on - strand, within HMPREF1058_RS04375at 49.337 kb on - strand, within HMPREF1058_RS04375at 49.338 kb on + strand, within HMPREF1058_RS04375at 49.408 kb on + strand, within HMPREF1058_RS04375at 49.408 kb on + strand, within HMPREF1058_RS04375at 49.409 kb on - strand, within HMPREF1058_RS04375at 49.503 kb on + strand, within HMPREF1058_RS04375at 49.528 kb on + strand, within HMPREF1058_RS04375at 49.610 kb on - strand, within HMPREF1058_RS04375at 49.775 kb on - strandat 49.833 kb on + strandat 49.834 kb on - strandat 49.860 kb on + strandat 49.864 kb on + strandat 49.865 kb on - strandat 49.866 kb on + strandat 49.876 kb on + strandat 49.876 kb on + strandat 49.877 kb on - strandat 49.878 kb on + strandat 49.878 kb on + strandat 49.953 kb on + strandat 49.954 kb on - strandat 49.956 kb on + strandat 49.956 kb on + strandat 50.004 kb on - strand, within HMPREF1058_RS04370at 50.023 kb on + strand, within HMPREF1058_RS04370at 50.068 kb on + strand, within HMPREF1058_RS04370at 50.101 kb on + strand, within HMPREF1058_RS04370at 50.169 kb on + strand, within HMPREF1058_RS04370at 50.170 kb on - strand, within HMPREF1058_RS04370at 50.233 kb on + strand, within HMPREF1058_RS04370at 50.234 kb on - strand, within HMPREF1058_RS04370at 50.234 kb on - strand, within HMPREF1058_RS04370at 50.322 kb on + strand, within HMPREF1058_RS04370at 50.322 kb on + strand, within HMPREF1058_RS04370at 50.334 kb on + strand, within HMPREF1058_RS04370at 50.545 kb on + strand, within HMPREF1058_RS04370at 50.701 kb on + strand, within HMPREF1058_RS04370at 50.701 kb on + strand, within HMPREF1058_RS04370at 50.709 kb on + strand, within HMPREF1058_RS04370at 50.709 kb on + strand, within HMPREF1058_RS04370at 50.714 kb on + strand, within HMPREF1058_RS04370at 50.714 kb on + strand, within HMPREF1058_RS04370at 50.714 kb on + strand, within HMPREF1058_RS04370at 50.715 kb on - strand, within HMPREF1058_RS04370at 50.715 kb on - strand, within HMPREF1058_RS04370at 50.818 kb on + strandat 50.818 kb on + strandat 50.819 kb on - strandat 50.851 kb on - strand

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Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse7; day4
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47,975 - HMPREF1058_RS04385 0.62 +2.6
48,170 + +1.4
48,170 + -0.2
48,199 + +0.9
48,200 - -0.8
48,202 - +2.2
48,207 + +1.2
48,254 - +1.1
48,261 + -0.4
48,270 - -1.8
48,290 - +2.1
48,294 + +1.0
48,294 + +1.6
48,336 + HMPREF1058_RS04380 0.12 +0.2
48,359 - HMPREF1058_RS04380 0.15 -1.5
48,361 - HMPREF1058_RS04380 0.16 -1.5
48,361 - HMPREF1058_RS04380 0.16 +1.1
48,361 - HMPREF1058_RS04380 0.16 +1.3
48,364 - HMPREF1058_RS04380 0.16 +1.0
48,441 + HMPREF1058_RS04380 0.29 -2.1
48,442 - HMPREF1058_RS04380 0.29 -0.8
48,443 + HMPREF1058_RS04380 0.30 -1.8
48,479 - HMPREF1058_RS04380 0.36 -1.0
48,479 - HMPREF1058_RS04380 0.36 -0.3
48,535 - HMPREF1058_RS04380 0.45 -2.6
48,594 - HMPREF1058_RS04380 0.55 -0.2
48,638 - HMPREF1058_RS04380 0.63 -3.0
48,638 - HMPREF1058_RS04380 0.63 -0.9
48,677 - HMPREF1058_RS04380 0.69 +1.0
48,685 - HMPREF1058_RS04380 0.71 +1.4
48,685 - HMPREF1058_RS04380 0.71 +0.2
48,699 - HMPREF1058_RS04380 0.73 +0.2
48,700 - HMPREF1058_RS04380 0.73 -1.0
48,827 - +0.4
48,874 + -2.4
48,885 + +0.2
48,886 - +0.5
48,909 - +0.2
48,970 + +0.5
49,086 + HMPREF1058_RS04375 0.13 -2.6
49,121 - HMPREF1058_RS04375 0.17 -4.5
49,276 + HMPREF1058_RS04375 0.34 +0.2
49,322 - HMPREF1058_RS04375 0.39 -2.1
49,322 - HMPREF1058_RS04375 0.39 -3.5
49,324 - HMPREF1058_RS04375 0.40 -3.6
49,330 - HMPREF1058_RS04375 0.40 -4.1
49,335 - HMPREF1058_RS04375 0.41 +0.2
49,335 - HMPREF1058_RS04375 0.41 +0.2
49,337 - HMPREF1058_RS04375 0.41 -5.3
49,337 - HMPREF1058_RS04375 0.41 -3.0
49,337 - HMPREF1058_RS04375 0.41 +0.2
49,338 + HMPREF1058_RS04375 0.41 -2.4
49,408 + HMPREF1058_RS04375 0.49 -1.4
49,408 + HMPREF1058_RS04375 0.49 +0.2
49,409 - HMPREF1058_RS04375 0.49 -3.6
49,503 + HMPREF1058_RS04375 0.60 -0.8
49,528 + HMPREF1058_RS04375 0.62 -4.0
49,610 - HMPREF1058_RS04375 0.72 -2.1
49,775 - -3.7
49,833 + -0.8
49,834 - +0.2
49,860 + -3.4
49,864 + -1.8
49,865 - -0.8
49,866 + -0.8
49,876 + -3.4
49,876 + -2.8
49,877 - -1.7
49,878 + -0.6
49,878 + -2.4
49,953 + -2.3
49,954 - +0.2
49,956 + -1.4
49,956 + -0.8
50,004 - HMPREF1058_RS04370 0.13 -1.4
50,023 + HMPREF1058_RS04370 0.15 -1.4
50,068 + HMPREF1058_RS04370 0.19 -1.4
50,101 + HMPREF1058_RS04370 0.22 -1.8
50,169 + HMPREF1058_RS04370 0.29 -3.5
50,170 - HMPREF1058_RS04370 0.29 -0.8
50,233 + HMPREF1058_RS04370 0.35 -0.8
50,234 - HMPREF1058_RS04370 0.35 -3.0
50,234 - HMPREF1058_RS04370 0.35 -1.2
50,322 + HMPREF1058_RS04370 0.44 -1.4
50,322 + HMPREF1058_RS04370 0.44 -0.8
50,334 + HMPREF1058_RS04370 0.45 -1.4
50,545 + HMPREF1058_RS04370 0.65 -2.8
50,701 + HMPREF1058_RS04370 0.80 -2.4
50,701 + HMPREF1058_RS04370 0.80 -2.4
50,709 + HMPREF1058_RS04370 0.81 -2.4
50,709 + HMPREF1058_RS04370 0.81 -0.4
50,714 + HMPREF1058_RS04370 0.82 -1.8
50,714 + HMPREF1058_RS04370 0.82 -2.1
50,714 + HMPREF1058_RS04370 0.82 +0.2
50,715 - HMPREF1058_RS04370 0.82 -1.8
50,715 - HMPREF1058_RS04370 0.82 -2.8
50,818 + -0.8
50,818 + -1.4
50,819 - -1.1
50,851 - -2.6

Or see this region's nucleotide sequence