Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day2
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_RS07850 and HMPREF1078_RS07855 are separated by 149 nucleotides HMPREF1078_RS07855 and HMPREF1078_RS07860 are separated by 562 nucleotides
HMPREF1078_RS07850: HMPREF1078_RS07850 - AAA family ATPase, at 125,239 to 126,417
_RS07850
HMPREF1078_RS07855: HMPREF1078_RS07855 - branched-chain amino acid aminotransferase, at 126,567 to 127,586
_RS07855
HMPREF1078_RS07860: HMPREF1078_RS07860 - methylenetetrahydrofolate reductase [NAD(P)H], at 128,149 to 129,099
_RS07860
Position (kb) 126
127
128 Strain fitness (log2 ratio) -4
-3
-2
-1
0
1
2
3 at 125.589 kb on - strand, within HMPREF1078_RS07850 at 125.597 kb on + strand, within HMPREF1078_RS07850 at 125.597 kb on + strand, within HMPREF1078_RS07850 at 125.598 kb on - strand, within HMPREF1078_RS07850 at 125.598 kb on - strand, within HMPREF1078_RS07850 at 125.598 kb on - strand, within HMPREF1078_RS07850 at 125.627 kb on - strand, within HMPREF1078_RS07850 at 125.627 kb on - strand, within HMPREF1078_RS07850 at 125.659 kb on - strand, within HMPREF1078_RS07850 at 125.685 kb on - strand, within HMPREF1078_RS07850 at 125.732 kb on - strand, within HMPREF1078_RS07850 at 125.732 kb on - strand, within HMPREF1078_RS07850 at 125.732 kb on - strand, within HMPREF1078_RS07850 at 125.736 kb on - strand, within HMPREF1078_RS07850 at 125.736 kb on - strand, within HMPREF1078_RS07850 at 125.747 kb on - strand, within HMPREF1078_RS07850 at 125.760 kb on + strand, within HMPREF1078_RS07850 at 125.761 kb on - strand, within HMPREF1078_RS07850 at 125.835 kb on - strand, within HMPREF1078_RS07850 at 125.835 kb on - strand, within HMPREF1078_RS07850 at 125.847 kb on - strand, within HMPREF1078_RS07850 at 125.906 kb on - strand, within HMPREF1078_RS07850 at 125.920 kb on - strand, within HMPREF1078_RS07850 at 125.920 kb on - strand, within HMPREF1078_RS07850 at 125.922 kb on - strand, within HMPREF1078_RS07850 at 125.988 kb on - strand, within HMPREF1078_RS07850 at 125.988 kb on - strand, within HMPREF1078_RS07850 at 126.084 kb on - strand, within HMPREF1078_RS07850 at 126.189 kb on + strand, within HMPREF1078_RS07850 at 126.189 kb on + strand, within HMPREF1078_RS07850 at 126.190 kb on - strand, within HMPREF1078_RS07850 at 126.190 kb on - strand, within HMPREF1078_RS07850 at 126.190 kb on - strand, within HMPREF1078_RS07850 at 126.190 kb on - strand, within HMPREF1078_RS07850 at 126.221 kb on - strand, within HMPREF1078_RS07850 at 126.221 kb on - strand, within HMPREF1078_RS07850 at 126.221 kb on - strand, within HMPREF1078_RS07850 at 126.221 kb on - strand, within HMPREF1078_RS07850 at 126.224 kb on + strand, within HMPREF1078_RS07850 at 126.238 kb on - strand, within HMPREF1078_RS07850 at 126.238 kb on - strand, within HMPREF1078_RS07850 at 126.238 kb on - strand, within HMPREF1078_RS07850 at 126.371 kb on + strand at 126.372 kb on - strand at 126.389 kb on + strand at 126.389 kb on + strand at 126.389 kb on + strand at 126.390 kb on - strand at 126.390 kb on - strand at 126.390 kb on - strand at 126.393 kb on + strand at 126.393 kb on + strand at 126.394 kb on - strand at 126.435 kb on - strand at 126.450 kb on - strand at 126.475 kb on - strand at 126.477 kb on - strand at 126.481 kb on - strand at 126.564 kb on + strand at 126.565 kb on - strand at 126.890 kb on - strand, within HMPREF1078_RS07855 at 127.047 kb on - strand, within HMPREF1078_RS07855 at 127.076 kb on - strand, within HMPREF1078_RS07855 at 127.089 kb on - strand, within HMPREF1078_RS07855 at 127.158 kb on - strand, within HMPREF1078_RS07855 at 127.448 kb on + strand, within HMPREF1078_RS07855 at 127.448 kb on + strand, within HMPREF1078_RS07855 at 127.601 kb on - strand at 127.702 kb on - strand at 127.702 kb on - strand at 127.726 kb on - strand at 127.730 kb on + strand at 127.769 kb on - strand at 127.780 kb on + strand at 127.792 kb on - strand at 127.802 kb on + strand at 127.802 kb on + strand at 127.802 kb on + strand at 127.803 kb on - strand at 127.852 kb on + strand at 127.852 kb on + strand at 127.853 kb on - strand at 127.853 kb on - strand at 127.853 kb on - strand at 127.862 kb on + strand at 127.863 kb on - strand at 127.863 kb on - strand at 127.896 kb on - strand at 127.905 kb on + strand at 127.905 kb on + strand at 127.905 kb on + strand at 127.906 kb on - strand at 127.906 kb on - strand at 127.929 kb on - strand at 127.981 kb on + strand at 127.982 kb on - strand at 127.988 kb on + strand at 128.074 kb on + strand at 128.087 kb on + strand at 128.087 kb on + strand at 128.088 kb on - strand at 128.088 kb on - strand at 128.104 kb on + strand at 128.119 kb on + strand at 128.120 kb on - strand at 128.120 kb on - strand at 128.137 kb on + strand at 128.145 kb on + strand at 128.157 kb on - strand at 128.172 kb on + strand at 128.184 kb on + strand at 128.232 kb on - strand at 128.232 kb on - strand at 128.232 kb on - strand at 128.240 kb on + strand at 128.240 kb on + strand at 128.241 kb on - strand at 128.242 kb on + strand at 128.244 kb on + strand, within HMPREF1078_RS07860 at 128.244 kb on + strand, within HMPREF1078_RS07860 at 128.244 kb on + strand, within HMPREF1078_RS07860 at 128.244 kb on + strand, within HMPREF1078_RS07860 at 128.245 kb on - strand, within HMPREF1078_RS07860 at 128.245 kb on - strand, within HMPREF1078_RS07860 at 128.245 kb on - strand, within HMPREF1078_RS07860 at 128.245 kb on - strand, within HMPREF1078_RS07860 at 128.252 kb on + strand, within HMPREF1078_RS07860 at 128.281 kb on + strand, within HMPREF1078_RS07860 at 128.281 kb on + strand, within HMPREF1078_RS07860 at 128.281 kb on + strand, within HMPREF1078_RS07860 at 128.282 kb on - strand, within HMPREF1078_RS07860 at 128.289 kb on + strand, within HMPREF1078_RS07860 at 128.289 kb on + strand, within HMPREF1078_RS07860 at 128.289 kb on + strand, within HMPREF1078_RS07860 at 128.289 kb on + strand, within HMPREF1078_RS07860 at 128.289 kb on + strand, within HMPREF1078_RS07860 at 128.290 kb on - strand, within HMPREF1078_RS07860 at 128.290 kb on - strand, within HMPREF1078_RS07860 at 128.291 kb on + strand, within HMPREF1078_RS07860 at 128.291 kb on + strand, within HMPREF1078_RS07860 at 128.292 kb on - strand, within HMPREF1078_RS07860 at 128.312 kb on - strand, within HMPREF1078_RS07860 at 128.313 kb on + strand, within HMPREF1078_RS07860 at 128.314 kb on - strand, within HMPREF1078_RS07860 at 128.314 kb on - strand, within HMPREF1078_RS07860 at 128.314 kb on - strand, within HMPREF1078_RS07860 at 128.314 kb on - strand, within HMPREF1078_RS07860 at 128.317 kb on + strand, within HMPREF1078_RS07860 at 128.318 kb on - strand, within HMPREF1078_RS07860 at 128.337 kb on + strand, within HMPREF1078_RS07860 at 128.337 kb on + strand, within HMPREF1078_RS07860 at 128.337 kb on + strand, within HMPREF1078_RS07860 at 128.337 kb on + strand, within HMPREF1078_RS07860 at 128.403 kb on + strand, within HMPREF1078_RS07860 at 128.407 kb on + strand, within HMPREF1078_RS07860 at 128.430 kb on + strand, within HMPREF1078_RS07860 at 128.431 kb on - strand, within HMPREF1078_RS07860 at 128.433 kb on + strand, within HMPREF1078_RS07860 at 128.433 kb on + strand, within HMPREF1078_RS07860 at 128.434 kb on - strand, within HMPREF1078_RS07860 at 128.434 kb on - strand, within HMPREF1078_RS07860 at 128.434 kb on - strand, within HMPREF1078_RS07860 at 128.434 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.436 kb on - strand, within HMPREF1078_RS07860 at 128.449 kb on - strand, within HMPREF1078_RS07860 at 128.467 kb on + strand, within HMPREF1078_RS07860 at 128.468 kb on - strand, within HMPREF1078_RS07860 at 128.468 kb on - strand, within HMPREF1078_RS07860 at 128.468 kb on - strand, within HMPREF1078_RS07860 at 128.501 kb on - strand, within HMPREF1078_RS07860 at 128.528 kb on + strand, within HMPREF1078_RS07860 at 128.528 kb on + strand, within HMPREF1078_RS07860 at 128.561 kb on + strand, within HMPREF1078_RS07860 at 128.561 kb on + strand, within HMPREF1078_RS07860 at 128.561 kb on + strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.562 kb on - strand, within HMPREF1078_RS07860 at 128.563 kb on + strand, within HMPREF1078_RS07860 at 128.563 kb on + strand, within HMPREF1078_RS07860 at 128.564 kb on - strand, within HMPREF1078_RS07860 at 128.564 kb on - strand, within HMPREF1078_RS07860 at 128.564 kb on - strand, within HMPREF1078_RS07860
Per-strain Table
Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day2 remove 125,589 - HMPREF1078_RS07850 0.30 -2.0 125,597 + HMPREF1078_RS07850 0.30 -0.7 125,597 + HMPREF1078_RS07850 0.30 +0.2 125,598 - HMPREF1078_RS07850 0.30 -1.7 125,598 - HMPREF1078_RS07850 0.30 +0.2 125,598 - HMPREF1078_RS07850 0.30 +2.5 125,627 - HMPREF1078_RS07850 0.33 -0.8 125,627 - HMPREF1078_RS07850 0.33 -2.5 125,659 - HMPREF1078_RS07850 0.36 -2.4 125,685 - HMPREF1078_RS07850 0.38 +1.6 125,732 - HMPREF1078_RS07850 0.42 -0.9 125,732 - HMPREF1078_RS07850 0.42 +1.7 125,732 - HMPREF1078_RS07850 0.42 -1.6 125,736 - HMPREF1078_RS07850 0.42 +1.1 125,736 - HMPREF1078_RS07850 0.42 -1.1 125,747 - HMPREF1078_RS07850 0.43 -2.9 125,760 + HMPREF1078_RS07850 0.44 +0.2 125,761 - HMPREF1078_RS07850 0.44 -2.3 125,835 - HMPREF1078_RS07850 0.51 +1.2 125,835 - HMPREF1078_RS07850 0.51 -0.1 125,847 - HMPREF1078_RS07850 0.52 +0.3 125,906 - HMPREF1078_RS07850 0.57 -0.7 125,920 - HMPREF1078_RS07850 0.58 -0.3 125,920 - HMPREF1078_RS07850 0.58 -0.6 125,922 - HMPREF1078_RS07850 0.58 -1.5 125,988 - HMPREF1078_RS07850 0.64 -1.4 125,988 - HMPREF1078_RS07850 0.64 -1.7 126,084 - HMPREF1078_RS07850 0.72 +0.2 126,189 + HMPREF1078_RS07850 0.81 +1.5 126,189 + HMPREF1078_RS07850 0.81 +1.5 126,190 - HMPREF1078_RS07850 0.81 +0.5 126,190 - HMPREF1078_RS07850 0.81 -2.8 126,190 - HMPREF1078_RS07850 0.81 -1.4 126,190 - HMPREF1078_RS07850 0.81 -0.5 126,221 - HMPREF1078_RS07850 0.83 +0.5 126,221 - HMPREF1078_RS07850 0.83 +0.4 126,221 - HMPREF1078_RS07850 0.83 -0.3 126,221 - HMPREF1078_RS07850 0.83 -1.1 126,224 + HMPREF1078_RS07850 0.84 +0.2 126,238 - HMPREF1078_RS07850 0.85 -0.2 126,238 - HMPREF1078_RS07850 0.85 +1.0 126,238 - HMPREF1078_RS07850 0.85 -0.8 126,371 + +0.2 126,372 - -2.1 126,389 + +0.5 126,389 + -0.3 126,389 + +0.5 126,390 - -1.2 126,390 - +1.3 126,390 - -2.8 126,393 + -0.1 126,393 + -0.3 126,394 - -0.2 126,435 - -0.7 126,450 - +2.5 126,475 - -2.3 126,477 - -1.2 126,481 - -0.1 126,564 + -2.9 126,565 - -1.1 126,890 - HMPREF1078_RS07855 0.32 -0.1 127,047 - HMPREF1078_RS07855 0.47 +0.5 127,076 - HMPREF1078_RS07855 0.50 +0.9 127,089 - HMPREF1078_RS07855 0.51 -0.1 127,158 - HMPREF1078_RS07855 0.58 +1.5 127,448 + HMPREF1078_RS07855 0.86 -0.8 127,448 + HMPREF1078_RS07855 0.86 -0.5 127,601 - -1.4 127,702 - -2.2 127,702 - -0.1 127,726 - +2.1 127,730 + -3.1 127,769 - +0.5 127,780 + -0.6 127,792 - +0.2 127,802 + +0.6 127,802 + -1.2 127,802 + -1.2 127,803 - -1.6 127,852 + +1.0 127,852 + +0.3 127,853 - +0.3 127,853 - +2.1 127,853 - +2.2 127,862 + +0.9 127,863 - -0.5 127,863 - -1.4 127,896 - -2.9 127,905 + -0.7 127,905 + +1.7 127,905 + -0.1 127,906 - -1.1 127,906 - +0.0 127,929 - -2.0 127,981 + -2.0 127,982 - -1.6 127,988 + +0.1 128,074 + -1.6 128,087 + -2.8 128,087 + +0.2 128,088 - -0.1 128,088 - +0.5 128,104 + +1.0 128,119 + +0.5 128,120 - -1.7 128,120 - -2.4 128,137 + +2.0 128,145 + -0.4 128,157 - +2.0 128,172 + -0.8 128,184 + +1.2 128,232 - +1.2 128,232 - -0.6 128,232 - -1.8 128,240 + -2.7 128,240 + -0.9 128,241 - -0.3 128,242 + +2.5 128,244 + HMPREF1078_RS07860 0.10 +0.7 128,244 + HMPREF1078_RS07860 0.10 +0.1 128,244 + HMPREF1078_RS07860 0.10 +0.3 128,244 + HMPREF1078_RS07860 0.10 -0.9 128,245 - HMPREF1078_RS07860 0.10 +2.7 128,245 - HMPREF1078_RS07860 0.10 -0.5 128,245 - HMPREF1078_RS07860 0.10 -1.7 128,245 - HMPREF1078_RS07860 0.10 +2.3 128,252 + HMPREF1078_RS07860 0.11 -1.7 128,281 + HMPREF1078_RS07860 0.14 -0.6 128,281 + HMPREF1078_RS07860 0.14 -0.5 128,281 + HMPREF1078_RS07860 0.14 +2.9 128,282 - HMPREF1078_RS07860 0.14 -2.5 128,289 + HMPREF1078_RS07860 0.15 +0.7 128,289 + HMPREF1078_RS07860 0.15 -3.4 128,289 + HMPREF1078_RS07860 0.15 -1.5 128,289 + HMPREF1078_RS07860 0.15 +0.4 128,289 + HMPREF1078_RS07860 0.15 +0.5 128,290 - HMPREF1078_RS07860 0.15 -2.5 128,290 - HMPREF1078_RS07860 0.15 +1.5 128,291 + HMPREF1078_RS07860 0.15 -0.8 128,291 + HMPREF1078_RS07860 0.15 -2.9 128,292 - HMPREF1078_RS07860 0.15 -1.9 128,312 - HMPREF1078_RS07860 0.17 +2.2 128,313 + HMPREF1078_RS07860 0.17 -1.4 128,314 - HMPREF1078_RS07860 0.17 +1.3 128,314 - HMPREF1078_RS07860 0.17 -1.7 128,314 - HMPREF1078_RS07860 0.17 -1.3 128,314 - HMPREF1078_RS07860 0.17 +0.7 128,317 + HMPREF1078_RS07860 0.18 -1.5 128,318 - HMPREF1078_RS07860 0.18 -2.3 128,337 + HMPREF1078_RS07860 0.20 +0.5 128,337 + HMPREF1078_RS07860 0.20 +0.3 128,337 + HMPREF1078_RS07860 0.20 -0.5 128,337 + HMPREF1078_RS07860 0.20 +0.2 128,403 + HMPREF1078_RS07860 0.27 +1.1 128,407 + HMPREF1078_RS07860 0.27 +2.7 128,430 + HMPREF1078_RS07860 0.30 -0.2 128,431 - HMPREF1078_RS07860 0.30 -0.8 128,433 + HMPREF1078_RS07860 0.30 +0.5 128,433 + HMPREF1078_RS07860 0.30 -0.8 128,434 - HMPREF1078_RS07860 0.30 -2.5 128,434 - HMPREF1078_RS07860 0.30 -1.5 128,434 - HMPREF1078_RS07860 0.30 +3.5 128,434 - HMPREF1078_RS07860 0.30 +0.2 128,436 - HMPREF1078_RS07860 0.30 -1.2 128,436 - HMPREF1078_RS07860 0.30 -1.5 128,436 - HMPREF1078_RS07860 0.30 -1.4 128,436 - HMPREF1078_RS07860 0.30 -2.6 128,436 - HMPREF1078_RS07860 0.30 +1.6 128,436 - HMPREF1078_RS07860 0.30 -0.8 128,436 - HMPREF1078_RS07860 0.30 -0.8 128,449 - HMPREF1078_RS07860 0.32 +2.3 128,467 + HMPREF1078_RS07860 0.33 -0.9 128,468 - HMPREF1078_RS07860 0.34 -2.8 128,468 - HMPREF1078_RS07860 0.34 +1.0 128,468 - HMPREF1078_RS07860 0.34 -0.1 128,501 - HMPREF1078_RS07860 0.37 -0.2 128,528 + HMPREF1078_RS07860 0.40 +3.1 128,528 + HMPREF1078_RS07860 0.40 +1.7 128,561 + HMPREF1078_RS07860 0.43 +0.7 128,561 + HMPREF1078_RS07860 0.43 -4.2 128,561 + HMPREF1078_RS07860 0.43 +0.4 128,562 - HMPREF1078_RS07860 0.43 -3.5 128,562 - HMPREF1078_RS07860 0.43 -1.1 128,562 - HMPREF1078_RS07860 0.43 -0.5 128,562 - HMPREF1078_RS07860 0.43 -1.2 128,562 - HMPREF1078_RS07860 0.43 +1.3 128,562 - HMPREF1078_RS07860 0.43 +0.2 128,562 - HMPREF1078_RS07860 0.43 +2.5 128,563 + HMPREF1078_RS07860 0.44 +1.0 128,563 + HMPREF1078_RS07860 0.44 +0.7 128,564 - HMPREF1078_RS07860 0.44 -0.7 128,564 - HMPREF1078_RS07860 0.44 -0.2 128,564 - HMPREF1078_RS07860 0.44 +0.2
Or see this region's nucleotide sequence