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_RS14995 and HMPREF1078_RS15000 are separated by 110 nucleotides HMPREF1078_RS15000 and HMPREF1078_RS15005 are separated by 401 nucleotides HMPREF1078_RS15005 and HMPREF1078_RS15010 overlap by 13 nucleotides
HMPREF1078_RS14995: HMPREF1078_RS14995 - BamA/TamA family outer membrane protein, at 52,080 to 54,428
_RS14995
HMPREF1078_RS15000: HMPREF1078_RS15000 - tRNA-Arg, at 54,539 to 54,612
_RS15000
HMPREF1078_RS15005: HMPREF1078_RS15005 - biosynthetic arginine decarboxylase, at 55,014 to 56,906
_RS15005
HMPREF1078_RS15010: HMPREF1078_RS15010 - DNA polymerase IV, at 56,894 to 57,988
_RS15010
Position (kb) 55
56
57 Strain fitness (log2 ratio) -5
-4
-3
-2
-1
0
1
2
3
4 at 54.034 kb on + strand, within HMPREF1078_RS14995 at 54.034 kb on + strand, within HMPREF1078_RS14995 at 54.035 kb on - strand, within HMPREF1078_RS14995 at 54.179 kb on + strand, within HMPREF1078_RS14995 at 54.271 kb on + strand at 54.332 kb on + strand at 54.390 kb on - strand at 54.444 kb on + strand at 54.444 kb on + strand at 54.445 kb on - strand at 54.445 kb on - strand at 54.448 kb on + strand at 54.448 kb on + strand at 54.457 kb on + strand at 54.457 kb on + strand at 54.458 kb on - strand at 54.461 kb on + strand at 54.461 kb on + strand at 54.637 kb on - strand at 54.650 kb on - strand at 54.666 kb on + strand at 54.668 kb on + strand at 54.669 kb on - strand at 54.685 kb on + strand at 54.685 kb on + strand at 54.686 kb on - strand at 54.692 kb on + strand at 54.693 kb on - strand at 54.708 kb on + strand at 54.708 kb on + strand at 54.708 kb on + strand at 54.709 kb on - strand at 54.709 kb on - strand at 54.709 kb on - strand at 54.709 kb on - strand at 54.709 kb on - strand at 54.754 kb on + strand at 54.755 kb on - strand at 54.760 kb on - strand at 54.783 kb on - strand at 54.847 kb on + strand at 54.880 kb on + strand at 54.881 kb on - strand at 54.881 kb on - strand at 54.881 kb on - strand at 54.881 kb on - strand at 54.882 kb on + strand at 54.884 kb on + strand at 54.885 kb on - strand at 54.889 kb on - strand at 54.896 kb on - strand at 54.898 kb on - strand at 54.902 kb on - strand at 54.915 kb on + strand at 54.919 kb on + strand at 54.920 kb on - strand at 54.935 kb on + strand at 54.936 kb on - strand at 54.936 kb on - strand at 54.936 kb on - strand at 54.936 kb on - strand at 54.962 kb on - strand at 54.965 kb on + strand at 54.966 kb on - strand at 54.966 kb on - strand at 54.966 kb on - strand at 55.050 kb on + strand at 55.050 kb on + strand at 55.050 kb on + strand at 55.077 kb on + strand at 55.077 kb on + strand at 55.078 kb on - strand at 55.078 kb on - strand at 55.085 kb on + strand at 55.085 kb on + strand at 55.086 kb on - strand at 55.105 kb on + strand at 55.105 kb on + strand at 55.105 kb on + strand at 55.112 kb on - strand at 55.172 kb on - strand at 55.192 kb on + strand at 55.192 kb on + strand at 55.211 kb on + strand, within HMPREF1078_RS15005 at 55.211 kb on + strand, within HMPREF1078_RS15005 at 55.269 kb on + strand, within HMPREF1078_RS15005 at 55.270 kb on - strand, within HMPREF1078_RS15005 at 55.295 kb on + strand, within HMPREF1078_RS15005 at 55.296 kb on - strand, within HMPREF1078_RS15005 at 55.370 kb on - strand, within HMPREF1078_RS15005 at 55.421 kb on + strand, within HMPREF1078_RS15005 at 55.421 kb on + strand, within HMPREF1078_RS15005 at 55.422 kb on - strand, within HMPREF1078_RS15005 at 55.443 kb on - strand, within HMPREF1078_RS15005 at 55.443 kb on - strand, within HMPREF1078_RS15005 at 55.455 kb on + strand, within HMPREF1078_RS15005 at 55.470 kb on + strand, within HMPREF1078_RS15005 at 55.470 kb on + strand, within HMPREF1078_RS15005 at 55.470 kb on + strand, within HMPREF1078_RS15005 at 55.470 kb on + strand, within HMPREF1078_RS15005 at 55.471 kb on - strand, within HMPREF1078_RS15005 at 55.481 kb on - strand, within HMPREF1078_RS15005 at 55.601 kb on + strand, within HMPREF1078_RS15005 at 55.628 kb on + strand, within HMPREF1078_RS15005 at 55.784 kb on + strand, within HMPREF1078_RS15005 at 55.819 kb on + strand, within HMPREF1078_RS15005 at 55.820 kb on - strand, within HMPREF1078_RS15005 at 55.884 kb on + strand, within HMPREF1078_RS15005 at 55.892 kb on + strand, within HMPREF1078_RS15005 at 55.893 kb on - strand, within HMPREF1078_RS15005 at 55.907 kb on + strand, within HMPREF1078_RS15005 at 55.926 kb on + strand, within HMPREF1078_RS15005 at 55.941 kb on + strand, within HMPREF1078_RS15005 at 55.942 kb on - strand, within HMPREF1078_RS15005 at 55.945 kb on + strand, within HMPREF1078_RS15005 at 55.945 kb on + strand, within HMPREF1078_RS15005 at 55.945 kb on + strand, within HMPREF1078_RS15005 at 55.955 kb on + strand, within HMPREF1078_RS15005 at 55.955 kb on + strand, within HMPREF1078_RS15005 at 55.961 kb on + strand, within HMPREF1078_RS15005 at 55.961 kb on + strand, within HMPREF1078_RS15005 at 55.961 kb on + strand, within HMPREF1078_RS15005 at 55.962 kb on - strand, within HMPREF1078_RS15005 at 55.992 kb on - strand, within HMPREF1078_RS15005 at 56.012 kb on - strand, within HMPREF1078_RS15005 at 56.057 kb on - strand, within HMPREF1078_RS15005 at 56.178 kb on - strand, within HMPREF1078_RS15005 at 56.209 kb on + strand, within HMPREF1078_RS15005 at 56.209 kb on + strand, within HMPREF1078_RS15005 at 56.210 kb on - strand, within HMPREF1078_RS15005 at 56.243 kb on + strand, within HMPREF1078_RS15005 at 56.283 kb on + strand, within HMPREF1078_RS15005 at 56.284 kb on - strand, within HMPREF1078_RS15005 at 56.284 kb on - strand, within HMPREF1078_RS15005 at 56.365 kb on + strand, within HMPREF1078_RS15005 at 56.380 kb on - strand, within HMPREF1078_RS15005 at 56.537 kb on + strand, within HMPREF1078_RS15005 at 56.538 kb on - strand, within HMPREF1078_RS15005 at 56.566 kb on + strand, within HMPREF1078_RS15005 at 56.573 kb on - strand, within HMPREF1078_RS15005 at 56.598 kb on + strand, within HMPREF1078_RS15005 at 56.598 kb on + strand, within HMPREF1078_RS15005 at 56.598 kb on + strand, within HMPREF1078_RS15005 at 56.598 kb on + strand, within HMPREF1078_RS15005 at 56.599 kb on - strand, within HMPREF1078_RS15005 at 56.599 kb on - strand, within HMPREF1078_RS15005 at 56.599 kb on - strand, within HMPREF1078_RS15005 at 56.601 kb on + strand, within HMPREF1078_RS15005 at 56.601 kb on + strand, within HMPREF1078_RS15005 at 56.601 kb on + strand, within HMPREF1078_RS15005 at 56.601 kb on + strand, within HMPREF1078_RS15005 at 56.602 kb on + strand, within HMPREF1078_RS15005 at 56.602 kb on - strand, within HMPREF1078_RS15005 at 56.602 kb on - strand, within HMPREF1078_RS15005 at 56.602 kb on - strand, within HMPREF1078_RS15005 at 56.602 kb on - strand, within HMPREF1078_RS15005 at 56.603 kb on + strand, within HMPREF1078_RS15005 at 56.628 kb on + strand, within HMPREF1078_RS15005 at 56.648 kb on + strand, within HMPREF1078_RS15005 at 56.649 kb on - strand, within HMPREF1078_RS15005 at 56.649 kb on - strand, within HMPREF1078_RS15005 at 56.670 kb on - strand, within HMPREF1078_RS15005 at 56.670 kb on - strand, within HMPREF1078_RS15005 at 56.706 kb on + strand, within HMPREF1078_RS15005 at 56.757 kb on + strand at 56.757 kb on + strand at 56.757 kb on + strand at 56.757 kb on + strand at 56.757 kb on + strand at 56.757 kb on + strand at 56.757 kb on + strand at 56.758 kb on - strand at 56.758 kb on - strand at 56.758 kb on - strand at 56.758 kb on - strand at 56.758 kb on - strand at 56.766 kb on + strand at 56.766 kb on + strand at 56.769 kb on - strand at 56.810 kb on + strand at 56.810 kb on + strand at 56.810 kb on + strand at 56.828 kb on + strand at 56.849 kb on + strand at 56.850 kb on - strand at 56.869 kb on - strand at 56.883 kb on + strand at 56.883 kb on + strand at 56.883 kb on + strand at 56.884 kb on - strand at 56.884 kb on - strand at 56.890 kb on - strand at 56.891 kb on + strand at 56.891 kb on + strand at 56.891 kb on + strand at 56.891 kb on + strand at 56.891 kb on + strand at 56.891 kb on + strand at 56.892 kb on - strand at 56.892 kb on - strand at 56.895 kb on + strand at 56.895 kb on + strand at 56.896 kb on - strand at 56.896 kb on - strand at 57.013 kb on + strand, within HMPREF1078_RS15010 at 57.014 kb on - strand, within HMPREF1078_RS15010 at 57.015 kb on + strand, within HMPREF1078_RS15010 at 57.016 kb on - strand, within HMPREF1078_RS15010 at 57.050 kb on + strand, within HMPREF1078_RS15010 at 57.050 kb on + strand, within HMPREF1078_RS15010 at 57.142 kb on + strand, within HMPREF1078_RS15010 at 57.143 kb on - strand, within HMPREF1078_RS15010 at 57.198 kb on + strand, within HMPREF1078_RS15010 at 57.198 kb on + strand, within HMPREF1078_RS15010 at 57.200 kb on + strand, within HMPREF1078_RS15010 at 57.200 kb on + strand, within HMPREF1078_RS15010 at 57.201 kb on - strand, within HMPREF1078_RS15010 at 57.247 kb on + strand, within HMPREF1078_RS15010 at 57.248 kb on - strand, within HMPREF1078_RS15010 at 57.248 kb on - strand, within HMPREF1078_RS15010 at 57.248 kb on - strand, within HMPREF1078_RS15010 at 57.296 kb on + strand, within HMPREF1078_RS15010 at 57.297 kb on - strand, within HMPREF1078_RS15010 at 57.297 kb on - strand, within HMPREF1078_RS15010 at 57.303 kb on - strand, within HMPREF1078_RS15010 at 57.324 kb on + strand, within HMPREF1078_RS15010 at 57.326 kb on + strand, within HMPREF1078_RS15010 at 57.404 kb on + strand, within HMPREF1078_RS15010 at 57.405 kb on - strand, within HMPREF1078_RS15010 at 57.557 kb on - strand, within HMPREF1078_RS15010 at 57.558 kb on + strand, within HMPREF1078_RS15010 at 57.558 kb on + strand, within HMPREF1078_RS15010 at 57.559 kb on - strand, within HMPREF1078_RS15010 at 57.559 kb on - strand, within HMPREF1078_RS15010 at 57.623 kb on + strand, within HMPREF1078_RS15010 at 57.624 kb on - strand, within HMPREF1078_RS15010 at 57.710 kb on - strand, within HMPREF1078_RS15010 at 57.753 kb on + strand, within HMPREF1078_RS15010 at 57.754 kb on - strand, within HMPREF1078_RS15010 at 57.754 kb on - strand, within HMPREF1078_RS15010 at 57.852 kb on + strand, within HMPREF1078_RS15010
Per-strain Table
Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day3 remove 54,034 + HMPREF1078_RS14995 0.83 -2.8 54,034 + HMPREF1078_RS14995 0.83 -3.9 54,035 - HMPREF1078_RS14995 0.83 -3.5 54,179 + HMPREF1078_RS14995 0.89 -2.9 54,271 + -2.5 54,332 + -1.4 54,390 - -3.5 54,444 + -0.5 54,444 + +0.7 54,445 - -1.2 54,445 - +0.5 54,448 + +2.1 54,448 + +0.4 54,457 + +1.1 54,457 + -1.0 54,458 - +1.6 54,461 + -0.4 54,461 + -1.0 54,637 - +0.4 54,650 - -2.2 54,666 + -2.0 54,668 + -0.7 54,669 - -1.0 54,685 + -1.4 54,685 + -1.2 54,686 - +1.7 54,692 + +0.3 54,693 - +0.2 54,708 + -0.6 54,708 + -1.2 54,708 + +1.1 54,709 - -0.0 54,709 - +0.2 54,709 - -1.1 54,709 - -0.2 54,709 - -1.2 54,754 + -1.3 54,755 - -0.2 54,760 - +1.1 54,783 - +2.6 54,847 + +1.8 54,880 + -1.4 54,881 - -1.2 54,881 - -1.2 54,881 - -3.4 54,881 - -2.0 54,882 + +2.5 54,884 + -3.3 54,885 - -2.9 54,889 - -3.4 54,896 - -1.8 54,898 - -3.5 54,902 - -3.7 54,915 + +0.3 54,919 + +0.7 54,920 - -3.1 54,935 + -0.4 54,936 - -1.6 54,936 - -0.2 54,936 - -0.7 54,936 - -0.7 54,962 - -3.9 54,965 + -1.4 54,966 - +0.6 54,966 - -3.8 54,966 - -4.7 55,050 + -3.7 55,050 + -3.7 55,050 + -3.5 55,077 + -2.7 55,077 + -3.4 55,078 - -1.3 55,078 - -3.9 55,085 + -1.8 55,085 + -2.5 55,086 - -2.0 55,105 + -2.4 55,105 + -1.2 55,105 + -0.4 55,112 - -3.7 55,172 - -2.9 55,192 + -3.1 55,192 + -0.8 55,211 + HMPREF1078_RS15005 0.10 -3.8 55,211 + HMPREF1078_RS15005 0.10 -2.7 55,269 + HMPREF1078_RS15005 0.13 -2.8 55,270 - HMPREF1078_RS15005 0.14 -3.0 55,295 + HMPREF1078_RS15005 0.15 -2.2 55,296 - HMPREF1078_RS15005 0.15 -3.9 55,370 - HMPREF1078_RS15005 0.19 -3.9 55,421 + HMPREF1078_RS15005 0.22 -1.2 55,421 + HMPREF1078_RS15005 0.22 -4.2 55,422 - HMPREF1078_RS15005 0.22 -3.6 55,443 - HMPREF1078_RS15005 0.23 -1.2 55,443 - HMPREF1078_RS15005 0.23 -2.9 55,455 + HMPREF1078_RS15005 0.23 -3.0 55,470 + HMPREF1078_RS15005 0.24 -3.1 55,470 + HMPREF1078_RS15005 0.24 -3.6 55,470 + HMPREF1078_RS15005 0.24 -2.6 55,470 + HMPREF1078_RS15005 0.24 -1.2 55,471 - HMPREF1078_RS15005 0.24 -4.3 55,481 - HMPREF1078_RS15005 0.25 -3.9 55,601 + HMPREF1078_RS15005 0.31 -1.7 55,628 + HMPREF1078_RS15005 0.32 -3.3 55,784 + HMPREF1078_RS15005 0.41 -4.5 55,819 + HMPREF1078_RS15005 0.43 -2.5 55,820 - HMPREF1078_RS15005 0.43 -3.2 55,884 + HMPREF1078_RS15005 0.46 -2.1 55,892 + HMPREF1078_RS15005 0.46 -2.9 55,893 - HMPREF1078_RS15005 0.46 -3.9 55,907 + HMPREF1078_RS15005 0.47 -4.3 55,926 + HMPREF1078_RS15005 0.48 -4.0 55,941 + HMPREF1078_RS15005 0.49 +0.6 55,942 - HMPREF1078_RS15005 0.49 -4.6 55,945 + HMPREF1078_RS15005 0.49 -2.6 55,945 + HMPREF1078_RS15005 0.49 -3.2 55,945 + HMPREF1078_RS15005 0.49 -2.1 55,955 + HMPREF1078_RS15005 0.50 -3.2 55,955 + HMPREF1078_RS15005 0.50 -4.7 55,961 + HMPREF1078_RS15005 0.50 -3.1 55,961 + HMPREF1078_RS15005 0.50 -3.2 55,961 + HMPREF1078_RS15005 0.50 -0.8 55,962 - HMPREF1078_RS15005 0.50 -1.7 55,992 - HMPREF1078_RS15005 0.52 -2.6 56,012 - HMPREF1078_RS15005 0.53 -5.6 56,057 - HMPREF1078_RS15005 0.55 -4.2 56,178 - HMPREF1078_RS15005 0.61 -2.7 56,209 + HMPREF1078_RS15005 0.63 -0.7 56,209 + HMPREF1078_RS15005 0.63 -3.2 56,210 - HMPREF1078_RS15005 0.63 -2.7 56,243 + HMPREF1078_RS15005 0.65 -0.4 56,283 + HMPREF1078_RS15005 0.67 -3.0 56,284 - HMPREF1078_RS15005 0.67 -3.1 56,284 - HMPREF1078_RS15005 0.67 -1.4 56,365 + HMPREF1078_RS15005 0.71 -1.0 56,380 - HMPREF1078_RS15005 0.72 -1.4 56,537 + HMPREF1078_RS15005 0.80 +0.2 56,538 - HMPREF1078_RS15005 0.81 -4.4 56,566 + HMPREF1078_RS15005 0.82 -2.4 56,573 - HMPREF1078_RS15005 0.82 -3.2 56,598 + HMPREF1078_RS15005 0.84 -3.0 56,598 + HMPREF1078_RS15005 0.84 -2.1 56,598 + HMPREF1078_RS15005 0.84 +0.0 56,598 + HMPREF1078_RS15005 0.84 -5.0 56,599 - HMPREF1078_RS15005 0.84 -0.4 56,599 - HMPREF1078_RS15005 0.84 -4.3 56,599 - HMPREF1078_RS15005 0.84 -1.4 56,601 + HMPREF1078_RS15005 0.84 -2.5 56,601 + HMPREF1078_RS15005 0.84 -3.2 56,601 + HMPREF1078_RS15005 0.84 -3.6 56,601 + HMPREF1078_RS15005 0.84 -0.7 56,602 + HMPREF1078_RS15005 0.84 -2.0 56,602 - HMPREF1078_RS15005 0.84 -2.8 56,602 - HMPREF1078_RS15005 0.84 -2.9 56,602 - HMPREF1078_RS15005 0.84 -0.4 56,602 - HMPREF1078_RS15005 0.84 -2.8 56,603 + HMPREF1078_RS15005 0.84 -3.0 56,628 + HMPREF1078_RS15005 0.85 -3.6 56,648 + HMPREF1078_RS15005 0.86 -0.9 56,649 - HMPREF1078_RS15005 0.86 -2.9 56,649 - HMPREF1078_RS15005 0.86 -1.2 56,670 - HMPREF1078_RS15005 0.87 -1.3 56,670 - HMPREF1078_RS15005 0.87 +0.0 56,706 + HMPREF1078_RS15005 0.89 -3.4 56,757 + -3.5 56,757 + -2.8 56,757 + -2.9 56,757 + -2.7 56,757 + -2.5 56,757 + -3.2 56,757 + -2.7 56,758 - -0.9 56,758 - -1.7 56,758 - -2.8 56,758 - -2.2 56,758 - -3.1 56,766 + -2.4 56,766 + +2.1 56,769 - -3.9 56,810 + -3.7 56,810 + -3.2 56,810 + -2.9 56,828 + -2.4 56,849 + -1.9 56,850 - -2.0 56,869 - -4.3 56,883 + -0.7 56,883 + -0.7 56,883 + -0.2 56,884 - -1.5 56,884 - +0.1 56,890 - -1.6 56,891 + -5.0 56,891 + -0.9 56,891 + -2.5 56,891 + +0.1 56,891 + -1.8 56,891 + -0.4 56,892 - -4.1 56,892 - -3.8 56,895 + -3.9 56,895 + -3.0 56,896 - -1.2 56,896 - -3.3 57,013 + HMPREF1078_RS15010 0.11 +1.7 57,014 - HMPREF1078_RS15010 0.11 +1.5 57,015 + HMPREF1078_RS15010 0.11 +2.1 57,016 - HMPREF1078_RS15010 0.11 +2.1 57,050 + HMPREF1078_RS15010 0.14 -0.4 57,050 + HMPREF1078_RS15010 0.14 +0.4 57,142 + HMPREF1078_RS15010 0.23 -1.2 57,143 - HMPREF1078_RS15010 0.23 +1.1 57,198 + HMPREF1078_RS15010 0.28 +1.1 57,198 + HMPREF1078_RS15010 0.28 +0.2 57,200 + HMPREF1078_RS15010 0.28 -0.6 57,200 + HMPREF1078_RS15010 0.28 -0.6 57,201 - HMPREF1078_RS15010 0.28 -1.2 57,247 + HMPREF1078_RS15010 0.32 +2.7 57,248 - HMPREF1078_RS15010 0.32 -0.0 57,248 - HMPREF1078_RS15010 0.32 -0.7 57,248 - HMPREF1078_RS15010 0.32 +1.8 57,296 + HMPREF1078_RS15010 0.37 -0.5 57,297 - HMPREF1078_RS15010 0.37 +0.9 57,297 - HMPREF1078_RS15010 0.37 +1.1 57,303 - HMPREF1078_RS15010 0.37 -0.9 57,324 + HMPREF1078_RS15010 0.39 +0.6 57,326 + HMPREF1078_RS15010 0.39 +1.7 57,404 + HMPREF1078_RS15010 0.47 +2.6 57,405 - HMPREF1078_RS15010 0.47 -0.6 57,557 - HMPREF1078_RS15010 0.61 -1.6 57,558 + HMPREF1078_RS15010 0.61 +0.5 57,558 + HMPREF1078_RS15010 0.61 -0.3 57,559 - HMPREF1078_RS15010 0.61 -0.1 57,559 - HMPREF1078_RS15010 0.61 -2.4 57,623 + HMPREF1078_RS15010 0.67 +4.0 57,624 - HMPREF1078_RS15010 0.67 +0.0 57,710 - HMPREF1078_RS15010 0.75 -0.1 57,753 + HMPREF1078_RS15010 0.78 +1.5 57,754 - HMPREF1078_RS15010 0.79 +0.0 57,754 - HMPREF1078_RS15010 0.79 -3.3 57,852 + HMPREF1078_RS15010 0.87 +1.1
Or see this region's nucleotide sequence