Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; day4
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_RS19865 and HMPREF1078_RS08165 are separated by 118 nucleotides HMPREF1078_RS08165 and HMPREF1078_RS19560 are separated by 177 nucleotides HMPREF1078_RS19560 and HMPREF1078_RS18645 are separated by 128 nucleotides HMPREF1078_RS18645 and HMPREF1078_RS08170 are separated by 210 nucleotides HMPREF1078_RS08170 and HMPREF1078_RS08175 are separated by 54 nucleotides
HMPREF1078_RS19865: HMPREF1078_RS19865 - hypothetical protein, at 201,442 to 201,696
_RS19865
HMPREF1078_RS08165: HMPREF1078_RS08165 - helix-turn-helix domain-containing protein, at 201,815 to 202,027
_RS08165
HMPREF1078_RS19560: HMPREF1078_RS19560 - Ppx/GppA family phosphatase, at 202,205 to 202,381
_RS19560
HMPREF1078_RS18645: HMPREF1078_RS18645 - transposase, at 202,510 to 202,638
_RS18645
HMPREF1078_RS08170: HMPREF1078_RS08170 - methylglyoxal synthase, at 202,849 to 203,385
_RS08170
HMPREF1078_RS08175: HMPREF1078_RS08175 - arginase family protein, at 203,440 to 204,249
_RS08175
Position (kb) 202
203 Strain fitness (log2 ratio) -4
-3
-2
-1
0
1
2 at 201.536 kb on + strand, within HMPREF1078_RS19865 at 201.537 kb on - strand, within HMPREF1078_RS19865 at 201.537 kb on - strand, within HMPREF1078_RS19865 at 201.541 kb on + strand, within HMPREF1078_RS19865 at 201.542 kb on - strand, within HMPREF1078_RS19865 at 201.542 kb on - strand, within HMPREF1078_RS19865 at 201.543 kb on + strand, within HMPREF1078_RS19865 at 201.543 kb on + strand, within HMPREF1078_RS19865 at 201.544 kb on - strand, within HMPREF1078_RS19865 at 201.544 kb on - strand, within HMPREF1078_RS19865 at 201.558 kb on + strand, within HMPREF1078_RS19865 at 201.558 kb on + strand, within HMPREF1078_RS19865 at 201.571 kb on - strand, within HMPREF1078_RS19865 at 201.581 kb on + strand, within HMPREF1078_RS19865 at 201.584 kb on + strand, within HMPREF1078_RS19865 at 201.585 kb on - strand, within HMPREF1078_RS19865 at 201.585 kb on - strand, within HMPREF1078_RS19865 at 201.610 kb on + strand, within HMPREF1078_RS19865 at 201.610 kb on + strand, within HMPREF1078_RS19865 at 201.641 kb on - strand, within HMPREF1078_RS19865 at 201.689 kb on + strand at 201.690 kb on - strand at 201.710 kb on + strand at 201.769 kb on + strand at 201.769 kb on + strand at 201.770 kb on - strand at 201.770 kb on - strand at 201.770 kb on - strand at 201.773 kb on + strand at 201.773 kb on + strand at 201.773 kb on + strand at 201.774 kb on - strand at 201.774 kb on - strand at 201.898 kb on - strand, within HMPREF1078_RS08165 at 201.901 kb on - strand, within HMPREF1078_RS08165 at 201.901 kb on - strand, within HMPREF1078_RS08165 at 201.904 kb on + strand, within HMPREF1078_RS08165 at 201.904 kb on + strand, within HMPREF1078_RS08165 at 201.905 kb on - strand, within HMPREF1078_RS08165 at 201.905 kb on - strand, within HMPREF1078_RS08165 at 202.062 kb on + strand at 202.066 kb on + strand at 202.067 kb on - strand at 202.154 kb on - strand at 202.202 kb on + strand at 202.203 kb on - strand at 202.222 kb on + strand at 202.249 kb on + strand, within HMPREF1078_RS19560 at 202.249 kb on + strand, within HMPREF1078_RS19560 at 202.249 kb on + strand, within HMPREF1078_RS19560 at 202.250 kb on - strand, within HMPREF1078_RS19560 at 202.278 kb on + strand, within HMPREF1078_RS19560 at 202.289 kb on - strand, within HMPREF1078_RS19560 at 202.304 kb on + strand, within HMPREF1078_RS19560 at 202.305 kb on - strand, within HMPREF1078_RS19560 at 202.306 kb on + strand, within HMPREF1078_RS19560 at 202.330 kb on - strand, within HMPREF1078_RS19560 at 202.330 kb on - strand, within HMPREF1078_RS19560 at 202.340 kb on - strand, within HMPREF1078_RS19560 at 202.362 kb on + strand, within HMPREF1078_RS19560 at 202.362 kb on + strand, within HMPREF1078_RS19560 at 202.363 kb on - strand, within HMPREF1078_RS19560 at 202.363 kb on - strand, within HMPREF1078_RS19560 at 202.363 kb on - strand, within HMPREF1078_RS19560 at 202.364 kb on + strand at 202.405 kb on - strand at 202.409 kb on - strand at 202.409 kb on - strand at 202.422 kb on + strand at 202.422 kb on + strand at 202.445 kb on + strand at 202.456 kb on - strand at 202.485 kb on + strand at 202.491 kb on + strand at 202.491 kb on + strand at 202.624 kb on - strand, within HMPREF1078_RS18645 at 202.630 kb on + strand at 202.631 kb on - strand at 202.631 kb on - strand at 202.637 kb on - strand at 202.716 kb on - strand at 202.722 kb on + strand at 202.723 kb on - strand at 202.757 kb on - strand at 202.765 kb on - strand at 202.778 kb on + strand at 202.778 kb on + strand at 202.779 kb on - strand at 202.782 kb on + strand at 202.782 kb on + strand at 202.782 kb on + strand at 202.783 kb on - strand at 202.783 kb on - strand at 202.783 kb on - strand at 202.796 kb on + strand at 202.796 kb on + strand at 202.812 kb on + strand at 202.812 kb on + strand at 202.813 kb on - strand at 202.822 kb on + strand at 202.823 kb on - strand at 202.823 kb on - strand at 202.824 kb on + strand at 202.824 kb on + strand at 202.828 kb on + strand at 202.828 kb on + strand at 202.828 kb on + strand at 202.828 kb on + strand at 202.837 kb on - strand at 202.837 kb on - strand at 202.843 kb on + strand at 202.843 kb on + strand at 202.843 kb on + strand at 202.864 kb on - strand at 202.912 kb on + strand, within HMPREF1078_RS08170 at 202.943 kb on + strand, within HMPREF1078_RS08170 at 202.943 kb on + strand, within HMPREF1078_RS08170 at 202.965 kb on + strand, within HMPREF1078_RS08170 at 202.973 kb on + strand, within HMPREF1078_RS08170 at 203.002 kb on - strand, within HMPREF1078_RS08170 at 203.004 kb on + strand, within HMPREF1078_RS08170 at 203.005 kb on - strand, within HMPREF1078_RS08170 at 203.044 kb on - strand, within HMPREF1078_RS08170 at 203.098 kb on + strand, within HMPREF1078_RS08170 at 203.116 kb on - strand, within HMPREF1078_RS08170 at 203.130 kb on - strand, within HMPREF1078_RS08170 at 203.130 kb on - strand, within HMPREF1078_RS08170 at 203.147 kb on - strand, within HMPREF1078_RS08170 at 203.252 kb on - strand, within HMPREF1078_RS08170 at 203.266 kb on - strand, within HMPREF1078_RS08170 at 203.271 kb on + strand, within HMPREF1078_RS08170 at 203.271 kb on + strand, within HMPREF1078_RS08170 at 203.272 kb on - strand, within HMPREF1078_RS08170 at 203.277 kb on - strand, within HMPREF1078_RS08170 at 203.290 kb on + strand, within HMPREF1078_RS08170 at 203.323 kb on + strand, within HMPREF1078_RS08170 at 203.323 kb on + strand, within HMPREF1078_RS08170 at 203.324 kb on - strand, within HMPREF1078_RS08170 at 203.324 kb on - strand, within HMPREF1078_RS08170 at 203.324 kb on - strand, within HMPREF1078_RS08170 at 203.324 kb on - strand, within HMPREF1078_RS08170 at 203.392 kb on - strand at 203.418 kb on + strand at 203.419 kb on - strand at 203.419 kb on - strand at 203.419 kb on - strand at 203.421 kb on - strand at 203.421 kb on - strand at 203.569 kb on + strand, within HMPREF1078_RS08175 at 203.569 kb on + strand, within HMPREF1078_RS08175 at 203.572 kb on + strand, within HMPREF1078_RS08175 at 203.573 kb on - strand, within HMPREF1078_RS08175
Per-strain Table
Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; day4 remove 201,536 + HMPREF1078_RS19865 0.37 +0.2 201,537 - HMPREF1078_RS19865 0.37 -1.8 201,537 - HMPREF1078_RS19865 0.37 -1.2 201,541 + HMPREF1078_RS19865 0.39 +2.0 201,542 - HMPREF1078_RS19865 0.39 +0.2 201,542 - HMPREF1078_RS19865 0.39 -0.6 201,543 + HMPREF1078_RS19865 0.40 -0.6 201,543 + HMPREF1078_RS19865 0.40 -1.2 201,544 - HMPREF1078_RS19865 0.40 +0.0 201,544 - HMPREF1078_RS19865 0.40 -0.3 201,558 + HMPREF1078_RS19865 0.45 +1.2 201,558 + HMPREF1078_RS19865 0.45 +1.2 201,571 - HMPREF1078_RS19865 0.51 -0.8 201,581 + HMPREF1078_RS19865 0.55 -2.6 201,584 + HMPREF1078_RS19865 0.56 +0.3 201,585 - HMPREF1078_RS19865 0.56 +0.4 201,585 - HMPREF1078_RS19865 0.56 +0.8 201,610 + HMPREF1078_RS19865 0.66 -2.4 201,610 + HMPREF1078_RS19865 0.66 -2.2 201,641 - HMPREF1078_RS19865 0.78 +0.2 201,689 + +0.8 201,690 - +1.2 201,710 + +1.0 201,769 + +2.4 201,769 + -1.3 201,770 - +0.6 201,770 - -1.3 201,770 - -0.6 201,773 + -1.2 201,773 + +0.2 201,773 + -0.6 201,774 - -0.3 201,774 - +2.7 201,898 - HMPREF1078_RS08165 0.39 +1.4 201,901 - HMPREF1078_RS08165 0.40 -0.2 201,901 - HMPREF1078_RS08165 0.40 +0.2 201,904 + HMPREF1078_RS08165 0.42 +0.4 201,904 + HMPREF1078_RS08165 0.42 -0.3 201,905 - HMPREF1078_RS08165 0.42 -1.1 201,905 - HMPREF1078_RS08165 0.42 -2.5 202,062 + +0.5 202,066 + -0.8 202,067 - -1.4 202,154 - -2.2 202,202 + -1.6 202,203 - +0.1 202,222 + -0.7 202,249 + HMPREF1078_RS19560 0.25 +0.0 202,249 + HMPREF1078_RS19560 0.25 -0.3 202,249 + HMPREF1078_RS19560 0.25 -0.5 202,250 - HMPREF1078_RS19560 0.25 +1.0 202,278 + HMPREF1078_RS19560 0.41 +0.9 202,289 - HMPREF1078_RS19560 0.47 -1.9 202,304 + HMPREF1078_RS19560 0.56 +0.1 202,305 - HMPREF1078_RS19560 0.56 +0.7 202,306 + HMPREF1078_RS19560 0.57 +0.2 202,330 - HMPREF1078_RS19560 0.71 -1.3 202,330 - HMPREF1078_RS19560 0.71 -0.3 202,340 - HMPREF1078_RS19560 0.76 -1.1 202,362 + HMPREF1078_RS19560 0.89 +0.8 202,362 + HMPREF1078_RS19560 0.89 -0.1 202,363 - HMPREF1078_RS19560 0.89 -0.1 202,363 - HMPREF1078_RS19560 0.89 -0.5 202,363 - HMPREF1078_RS19560 0.89 -1.3 202,364 + +0.4 202,405 - -0.5 202,409 - -1.2 202,409 - +0.7 202,422 + +0.2 202,422 + -1.9 202,445 + -0.3 202,456 - +1.8 202,485 + -2.7 202,491 + +0.2 202,491 + -1.9 202,624 - HMPREF1078_RS18645 0.88 -1.8 202,630 + -0.8 202,631 - -3.0 202,631 - +0.6 202,637 - +0.2 202,716 - -1.1 202,722 + -0.6 202,723 - +0.7 202,757 - -0.1 202,765 - -1.9 202,778 + +1.2 202,778 + +0.1 202,779 - +0.7 202,782 + +0.9 202,782 + +1.8 202,782 + +0.9 202,783 - +0.7 202,783 - +0.1 202,783 - +0.2 202,796 + +0.7 202,796 + +0.4 202,812 + +1.0 202,812 + -3.3 202,813 - -2.9 202,822 + +0.5 202,823 - -1.3 202,823 - -2.9 202,824 + -0.3 202,824 + -1.8 202,828 + +1.6 202,828 + -2.1 202,828 + -3.9 202,828 + -2.6 202,837 - -0.3 202,837 - -1.1 202,843 + -0.8 202,843 + -0.3 202,843 + +0.7 202,864 - +1.0 202,912 + HMPREF1078_RS08170 0.12 +1.2 202,943 + HMPREF1078_RS08170 0.18 -0.3 202,943 + HMPREF1078_RS08170 0.18 +0.5 202,965 + HMPREF1078_RS08170 0.22 -0.3 202,973 + HMPREF1078_RS08170 0.23 -0.3 203,002 - HMPREF1078_RS08170 0.28 +0.4 203,004 + HMPREF1078_RS08170 0.29 -0.7 203,005 - HMPREF1078_RS08170 0.29 -1.8 203,044 - HMPREF1078_RS08170 0.36 -0.1 203,098 + HMPREF1078_RS08170 0.46 +2.2 203,116 - HMPREF1078_RS08170 0.50 -2.7 203,130 - HMPREF1078_RS08170 0.52 -2.5 203,130 - HMPREF1078_RS08170 0.52 +0.7 203,147 - HMPREF1078_RS08170 0.55 -0.5 203,252 - HMPREF1078_RS08170 0.75 -0.8 203,266 - HMPREF1078_RS08170 0.78 +1.0 203,271 + HMPREF1078_RS08170 0.79 +0.2 203,271 + HMPREF1078_RS08170 0.79 +1.2 203,272 - HMPREF1078_RS08170 0.79 +0.2 203,277 - HMPREF1078_RS08170 0.80 +0.7 203,290 + HMPREF1078_RS08170 0.82 +0.5 203,323 + HMPREF1078_RS08170 0.88 +1.2 203,323 + HMPREF1078_RS08170 0.88 +0.2 203,324 - HMPREF1078_RS08170 0.88 +0.4 203,324 - HMPREF1078_RS08170 0.88 -0.8 203,324 - HMPREF1078_RS08170 0.88 -0.0 203,324 - HMPREF1078_RS08170 0.88 -0.3 203,392 - -0.3 203,418 + -0.3 203,419 - -1.1 203,419 - -1.5 203,419 - -0.7 203,421 - -1.2 203,421 - -0.8 203,569 + HMPREF1078_RS08175 0.16 -1.1 203,569 + HMPREF1078_RS08175 0.16 +0.5 203,572 + HMPREF1078_RS08175 0.16 -2.8 203,573 - HMPREF1078_RS08175 0.16 -2.9
Or see this region's nucleotide sequence