Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day3
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.
500 nt HMPREF1078_RS13180 and HMPREF1078_RS13185 are separated by 121 nucleotides HMPREF1078_RS13185 and HMPREF1078_RS13190 are separated by 19 nucleotides
HMPREF1078_RS13180: HMPREF1078_RS13180 - nucleoside triphosphate pyrophosphohydrolase, at 61,118 to 61,903
_RS13180
HMPREF1078_RS13185: HMPREF1078_RS13185 - cytochrome c biogenesis protein CcdA, at 62,025 to 64,118
_RS13185
HMPREF1078_RS13190: HMPREF1078_RS13190 - RluA family pseudouridine synthase, at 64,138 to 65,049
_RS13190
Position (kb) 62
63
64
65 Strain fitness (log2 ratio) -5
-4
-3
-2
-1
0
1
2
3
4 at 61.026 kb on + strand at 61.026 kb on + strand at 61.030 kb on - strand at 61.030 kb on - strand at 61.030 kb on - strand at 61.035 kb on + strand at 61.035 kb on + strand at 61.036 kb on - strand at 61.036 kb on - strand at 61.036 kb on - strand at 61.036 kb on - strand at 61.058 kb on + strand at 61.059 kb on - strand at 61.059 kb on - strand at 61.072 kb on - strand at 61.076 kb on + strand at 61.077 kb on - strand at 61.120 kb on - strand at 61.121 kb on + strand at 61.121 kb on + strand at 61.122 kb on - strand at 61.174 kb on + strand at 61.174 kb on + strand at 61.175 kb on - strand at 61.175 kb on - strand at 61.201 kb on + strand, within HMPREF1078_RS13180 at 61.202 kb on - strand, within HMPREF1078_RS13180 at 61.204 kb on + strand, within HMPREF1078_RS13180 at 61.204 kb on + strand, within HMPREF1078_RS13180 at 61.205 kb on - strand, within HMPREF1078_RS13180 at 61.205 kb on - strand, within HMPREF1078_RS13180 at 61.205 kb on - strand, within HMPREF1078_RS13180 at 61.205 kb on - strand, within HMPREF1078_RS13180 at 61.218 kb on + strand, within HMPREF1078_RS13180 at 61.280 kb on - strand, within HMPREF1078_RS13180 at 61.281 kb on + strand, within HMPREF1078_RS13180 at 61.281 kb on + strand, within HMPREF1078_RS13180 at 61.281 kb on + strand, within HMPREF1078_RS13180 at 61.281 kb on + strand, within HMPREF1078_RS13180 at 61.282 kb on - strand, within HMPREF1078_RS13180 at 61.339 kb on + strand, within HMPREF1078_RS13180 at 61.339 kb on + strand, within HMPREF1078_RS13180 at 61.340 kb on - strand, within HMPREF1078_RS13180 at 61.340 kb on - strand, within HMPREF1078_RS13180 at 61.612 kb on - strand, within HMPREF1078_RS13180 at 61.612 kb on - strand, within HMPREF1078_RS13180 at 61.687 kb on - strand, within HMPREF1078_RS13180 at 61.687 kb on - strand, within HMPREF1078_RS13180 at 61.687 kb on - strand, within HMPREF1078_RS13180 at 61.733 kb on - strand, within HMPREF1078_RS13180 at 61.771 kb on - strand, within HMPREF1078_RS13180 at 61.771 kb on - strand, within HMPREF1078_RS13180 at 61.787 kb on - strand, within HMPREF1078_RS13180 at 61.816 kb on + strand, within HMPREF1078_RS13180 at 62.018 kb on + strand at 62.018 kb on + strand at 62.018 kb on + strand at 62.018 kb on + strand at 62.026 kb on + strand at 62.027 kb on - strand at 62.031 kb on - strand at 62.048 kb on + strand at 62.048 kb on + strand at 62.048 kb on + strand at 62.049 kb on - strand at 62.053 kb on - strand at 62.082 kb on - strand at 62.082 kb on - strand at 62.083 kb on + strand at 62.110 kb on + strand at 62.181 kb on - strand at 62.181 kb on - strand at 62.183 kb on + strand at 62.184 kb on - strand at 62.195 kb on - strand at 62.276 kb on + strand, within HMPREF1078_RS13185 at 62.277 kb on - strand, within HMPREF1078_RS13185 at 62.305 kb on + strand, within HMPREF1078_RS13185 at 62.305 kb on + strand, within HMPREF1078_RS13185 at 62.306 kb on - strand, within HMPREF1078_RS13185 at 62.306 kb on - strand, within HMPREF1078_RS13185 at 62.306 kb on - strand, within HMPREF1078_RS13185 at 62.320 kb on - strand, within HMPREF1078_RS13185 at 62.500 kb on + strand, within HMPREF1078_RS13185 at 62.501 kb on - strand, within HMPREF1078_RS13185 at 62.561 kb on + strand, within HMPREF1078_RS13185 at 62.562 kb on - strand, within HMPREF1078_RS13185 at 62.563 kb on + strand, within HMPREF1078_RS13185 at 62.564 kb on - strand, within HMPREF1078_RS13185 at 62.614 kb on - strand, within HMPREF1078_RS13185 at 62.614 kb on - strand, within HMPREF1078_RS13185 at 62.617 kb on + strand, within HMPREF1078_RS13185 at 62.618 kb on - strand, within HMPREF1078_RS13185 at 62.618 kb on - strand, within HMPREF1078_RS13185 at 62.618 kb on - strand, within HMPREF1078_RS13185 at 62.652 kb on - strand, within HMPREF1078_RS13185 at 62.662 kb on + strand, within HMPREF1078_RS13185 at 62.678 kb on + strand, within HMPREF1078_RS13185 at 62.703 kb on - strand, within HMPREF1078_RS13185 at 62.790 kb on + strand, within HMPREF1078_RS13185 at 62.790 kb on + strand, within HMPREF1078_RS13185 at 62.791 kb on - strand, within HMPREF1078_RS13185 at 62.880 kb on - strand, within HMPREF1078_RS13185 at 62.923 kb on - strand, within HMPREF1078_RS13185 at 63.029 kb on + strand, within HMPREF1078_RS13185 at 63.065 kb on + strand, within HMPREF1078_RS13185 at 63.084 kb on + strand, within HMPREF1078_RS13185 at 63.084 kb on + strand, within HMPREF1078_RS13185 at 63.085 kb on - strand, within HMPREF1078_RS13185 at 63.126 kb on + strand, within HMPREF1078_RS13185 at 63.127 kb on - strand, within HMPREF1078_RS13185 at 63.127 kb on - strand, within HMPREF1078_RS13185 at 63.129 kb on + strand, within HMPREF1078_RS13185 at 63.144 kb on + strand, within HMPREF1078_RS13185 at 63.145 kb on - strand, within HMPREF1078_RS13185 at 63.145 kb on - strand, within HMPREF1078_RS13185 at 63.149 kb on + strand, within HMPREF1078_RS13185 at 63.199 kb on - strand, within HMPREF1078_RS13185 at 63.201 kb on - strand, within HMPREF1078_RS13185 at 63.230 kb on - strand, within HMPREF1078_RS13185 at 63.230 kb on - strand, within HMPREF1078_RS13185 at 63.270 kb on + strand, within HMPREF1078_RS13185 at 63.337 kb on - strand, within HMPREF1078_RS13185 at 63.533 kb on + strand, within HMPREF1078_RS13185 at 63.663 kb on + strand, within HMPREF1078_RS13185 at 63.812 kb on - strand, within HMPREF1078_RS13185 at 63.845 kb on - strand, within HMPREF1078_RS13185 at 63.846 kb on + strand, within HMPREF1078_RS13185 at 63.847 kb on - strand, within HMPREF1078_RS13185 at 63.958 kb on + strand at 63.958 kb on + strand at 63.959 kb on - strand at 64.032 kb on + strand at 64.033 kb on - strand at 64.033 kb on - strand at 64.033 kb on - strand at 64.104 kb on - strand at 64.139 kb on + strand at 64.140 kb on - strand at 64.155 kb on + strand at 64.156 kb on - strand at 64.271 kb on + strand, within HMPREF1078_RS13190 at 64.272 kb on - strand, within HMPREF1078_RS13190 at 64.272 kb on - strand, within HMPREF1078_RS13190 at 64.368 kb on - strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.436 kb on + strand, within HMPREF1078_RS13190 at 64.437 kb on - strand, within HMPREF1078_RS13190 at 64.437 kb on - strand, within HMPREF1078_RS13190 at 64.437 kb on - strand, within HMPREF1078_RS13190 at 64.437 kb on - strand, within HMPREF1078_RS13190 at 64.477 kb on + strand, within HMPREF1078_RS13190 at 64.478 kb on - strand, within HMPREF1078_RS13190 at 64.520 kb on + strand, within HMPREF1078_RS13190 at 64.520 kb on + strand, within HMPREF1078_RS13190 at 64.520 kb on + strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.521 kb on - strand, within HMPREF1078_RS13190 at 64.637 kb on - strand, within HMPREF1078_RS13190 at 64.637 kb on - strand, within HMPREF1078_RS13190 at 64.637 kb on - strand, within HMPREF1078_RS13190 at 64.644 kb on + strand, within HMPREF1078_RS13190 at 64.667 kb on + strand, within HMPREF1078_RS13190 at 64.668 kb on - strand, within HMPREF1078_RS13190 at 64.825 kb on + strand, within HMPREF1078_RS13190 at 64.927 kb on - strand, within HMPREF1078_RS13190 at 64.963 kb on + strand at 64.968 kb on + strand at 64.969 kb on - strand at 64.992 kb on + strand at 65.017 kb on - strand at 65.031 kb on - strand at 65.056 kb on - strand at 65.060 kb on - strand at 65.060 kb on - strand at 65.060 kb on - strand at 65.061 kb on + strand at 65.061 kb on + strand at 65.061 kb on + strand at 65.062 kb on - strand at 65.062 kb on - strand at 65.064 kb on - strand at 65.065 kb on + strand at 65.071 kb on - strand at 65.078 kb on + strand
Per-strain Table
Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day3 remove 61,026 + +3.5 61,026 + +2.2 61,030 - +1.8 61,030 - +2.2 61,030 - +2.8 61,035 + +2.5 61,035 + -2.7 61,036 - +2.7 61,036 - +3.1 61,036 - +0.4 61,036 - +1.4 61,058 + +1.9 61,059 - +0.2 61,059 - +1.6 61,072 - +3.5 61,076 + +1.4 61,077 - +2.4 61,120 - +2.7 61,121 + +0.5 61,121 + -0.3 61,122 - -1.9 61,174 + -0.7 61,174 + -1.3 61,175 - +1.2 61,175 - +1.4 61,201 + HMPREF1078_RS13180 0.11 +1.3 61,202 - HMPREF1078_RS13180 0.11 -0.6 61,204 + HMPREF1078_RS13180 0.11 -0.2 61,204 + HMPREF1078_RS13180 0.11 +4.3 61,205 - HMPREF1078_RS13180 0.11 -0.1 61,205 - HMPREF1078_RS13180 0.11 +2.1 61,205 - HMPREF1078_RS13180 0.11 +0.6 61,205 - HMPREF1078_RS13180 0.11 +1.3 61,218 + HMPREF1078_RS13180 0.13 -2.0 61,280 - HMPREF1078_RS13180 0.21 +2.1 61,281 + HMPREF1078_RS13180 0.21 +1.5 61,281 + HMPREF1078_RS13180 0.21 -1.3 61,281 + HMPREF1078_RS13180 0.21 +0.2 61,281 + HMPREF1078_RS13180 0.21 +0.4 61,282 - HMPREF1078_RS13180 0.21 +2.4 61,339 + HMPREF1078_RS13180 0.28 +1.2 61,339 + HMPREF1078_RS13180 0.28 +0.5 61,340 - HMPREF1078_RS13180 0.28 +3.7 61,340 - HMPREF1078_RS13180 0.28 -2.2 61,612 - HMPREF1078_RS13180 0.63 +1.7 61,612 - HMPREF1078_RS13180 0.63 +1.0 61,687 - HMPREF1078_RS13180 0.72 +2.1 61,687 - HMPREF1078_RS13180 0.72 +0.1 61,687 - HMPREF1078_RS13180 0.72 +4.1 61,733 - HMPREF1078_RS13180 0.78 -0.2 61,771 - HMPREF1078_RS13180 0.83 -0.4 61,771 - HMPREF1078_RS13180 0.83 -2.0 61,787 - HMPREF1078_RS13180 0.85 -0.6 61,816 + HMPREF1078_RS13180 0.89 +2.0 62,018 + +1.9 62,018 + -2.8 62,018 + -1.1 62,018 + -2.8 62,026 + +3.3 62,027 - +0.5 62,031 - -2.0 62,048 + -4.0 62,048 + -0.8 62,048 + +0.0 62,049 - +1.5 62,053 - +1.6 62,082 - -4.0 62,082 - -4.4 62,083 + -5.1 62,110 + -3.8 62,181 - -0.6 62,181 - -2.6 62,183 + -2.3 62,184 - -3.5 62,195 - -1.0 62,276 + HMPREF1078_RS13185 0.12 -0.1 62,277 - HMPREF1078_RS13185 0.12 -3.1 62,305 + HMPREF1078_RS13185 0.13 -3.7 62,305 + HMPREF1078_RS13185 0.13 -0.8 62,306 - HMPREF1078_RS13185 0.13 -3.2 62,306 - HMPREF1078_RS13185 0.13 -2.8 62,306 - HMPREF1078_RS13185 0.13 -4.3 62,320 - HMPREF1078_RS13185 0.14 -0.6 62,500 + HMPREF1078_RS13185 0.23 -4.0 62,501 - HMPREF1078_RS13185 0.23 -2.2 62,561 + HMPREF1078_RS13185 0.26 -0.8 62,562 - HMPREF1078_RS13185 0.26 -1.1 62,563 + HMPREF1078_RS13185 0.26 -2.8 62,564 - HMPREF1078_RS13185 0.26 -1.8 62,614 - HMPREF1078_RS13185 0.28 -2.0 62,614 - HMPREF1078_RS13185 0.28 -3.2 62,617 + HMPREF1078_RS13185 0.28 -2.8 62,618 - HMPREF1078_RS13185 0.28 -1.4 62,618 - HMPREF1078_RS13185 0.28 -1.7 62,618 - HMPREF1078_RS13185 0.28 -1.6 62,652 - HMPREF1078_RS13185 0.30 -2.4 62,662 + HMPREF1078_RS13185 0.30 -2.6 62,678 + HMPREF1078_RS13185 0.31 -2.8 62,703 - HMPREF1078_RS13185 0.32 -3.4 62,790 + HMPREF1078_RS13185 0.37 -1.6 62,790 + HMPREF1078_RS13185 0.37 -2.7 62,791 - HMPREF1078_RS13185 0.37 -2.3 62,880 - HMPREF1078_RS13185 0.41 -3.2 62,923 - HMPREF1078_RS13185 0.43 -2.3 63,029 + HMPREF1078_RS13185 0.48 +0.2 63,065 + HMPREF1078_RS13185 0.50 -1.5 63,084 + HMPREF1078_RS13185 0.51 -2.0 63,084 + HMPREF1078_RS13185 0.51 -0.8 63,085 - HMPREF1078_RS13185 0.51 -1.5 63,126 + HMPREF1078_RS13185 0.53 -3.2 63,127 - HMPREF1078_RS13185 0.53 -3.4 63,127 - HMPREF1078_RS13185 0.53 -1.1 63,129 + HMPREF1078_RS13185 0.53 -1.8 63,144 + HMPREF1078_RS13185 0.53 -1.3 63,145 - HMPREF1078_RS13185 0.53 -2.4 63,145 - HMPREF1078_RS13185 0.53 -0.8 63,149 + HMPREF1078_RS13185 0.54 -2.3 63,199 - HMPREF1078_RS13185 0.56 -3.0 63,201 - HMPREF1078_RS13185 0.56 -2.3 63,230 - HMPREF1078_RS13185 0.58 -1.7 63,230 - HMPREF1078_RS13185 0.58 -1.6 63,270 + HMPREF1078_RS13185 0.59 -2.3 63,337 - HMPREF1078_RS13185 0.63 -1.3 63,533 + HMPREF1078_RS13185 0.72 -3.8 63,663 + HMPREF1078_RS13185 0.78 -2.4 63,812 - HMPREF1078_RS13185 0.85 -4.2 63,845 - HMPREF1078_RS13185 0.87 -3.3 63,846 + HMPREF1078_RS13185 0.87 -1.3 63,847 - HMPREF1078_RS13185 0.87 -2.9 63,958 + -2.0 63,958 + -4.6 63,959 - +0.2 64,032 + -1.5 64,033 - -3.7 64,033 - -1.3 64,033 - -3.2 64,104 - -3.4 64,139 + -4.3 64,140 - -0.0 64,155 + -2.3 64,156 - +1.5 64,271 + HMPREF1078_RS13190 0.15 -2.8 64,272 - HMPREF1078_RS13190 0.15 +0.6 64,272 - HMPREF1078_RS13190 0.15 -1.6 64,368 - HMPREF1078_RS13190 0.25 -2.1 64,436 + HMPREF1078_RS13190 0.33 -3.3 64,436 + HMPREF1078_RS13190 0.33 -2.3 64,436 + HMPREF1078_RS13190 0.33 -1.0 64,436 + HMPREF1078_RS13190 0.33 -0.8 64,436 + HMPREF1078_RS13190 0.33 -3.7 64,436 + HMPREF1078_RS13190 0.33 -4.9 64,437 - HMPREF1078_RS13190 0.33 +0.4 64,437 - HMPREF1078_RS13190 0.33 -0.1 64,437 - HMPREF1078_RS13190 0.33 +1.9 64,437 - HMPREF1078_RS13190 0.33 +0.5 64,477 + HMPREF1078_RS13190 0.37 -3.2 64,478 - HMPREF1078_RS13190 0.37 -1.5 64,520 + HMPREF1078_RS13190 0.42 -2.1 64,520 + HMPREF1078_RS13190 0.42 -2.3 64,520 + HMPREF1078_RS13190 0.42 -2.0 64,521 - HMPREF1078_RS13190 0.42 -2.4 64,521 - HMPREF1078_RS13190 0.42 +1.0 64,521 - HMPREF1078_RS13190 0.42 -2.5 64,521 - HMPREF1078_RS13190 0.42 -2.9 64,521 - HMPREF1078_RS13190 0.42 +1.9 64,521 - HMPREF1078_RS13190 0.42 +1.8 64,637 - HMPREF1078_RS13190 0.55 +0.2 64,637 - HMPREF1078_RS13190 0.55 +0.2 64,637 - HMPREF1078_RS13190 0.55 -0.3 64,644 + HMPREF1078_RS13190 0.55 -3.7 64,667 + HMPREF1078_RS13190 0.58 -4.7 64,668 - HMPREF1078_RS13190 0.58 -0.4 64,825 + HMPREF1078_RS13190 0.75 -3.8 64,927 - HMPREF1078_RS13190 0.87 +0.8 64,963 + -2.7 64,968 + -4.1 64,969 - -0.8 64,992 + -0.1 65,017 - -0.3 65,031 - -0.9 65,056 - +0.2 65,060 - +1.4 65,060 - -0.4 65,060 - +2.8 65,061 + -3.8 65,061 + -3.6 65,061 + -3.1 65,062 - +0.2 65,062 - +1.5 65,064 - +1.5 65,065 + -3.3 65,071 - -3.1 65,078 + -2.7
Or see this region's nucleotide sequence