Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=MixComm; mouse2; day6
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 HMPREF1058_RS10425 and HMPREF1058_RS10420 are separated by 5 nucleotides HMPREF1058_RS10420 and HMPREF1058_RS10415 overlap by 1 nucleotides HMPREF1058_RS10415 and HMPREF1058_RS10410 overlap by 20 nucleotides HMPREF1058_RS10410 and HMPREF1058_RS10405 are separated by 297 nucleotides
HMPREF1058_RS10425: HMPREF1058_RS10425 - hypothetical protein, at 670,674 to 674,690
_RS10425
HMPREF1058_RS10420: HMPREF1058_RS10420 - hypothetical protein, at 674,696 to 675,010
_RS10420
HMPREF1058_RS10415: HMPREF1058_RS10415 - hypothetical protein, at 675,010 to 675,387
_RS10415
HMPREF1058_RS10410: HMPREF1058_RS10410 - reverse transcriptase, at 675,368 to 676,408
_RS10410
HMPREF1058_RS10405: HMPREF1058_RS10405 - hypothetical protein, at 676,706 to 678,133
_RS10405
Position (kb) 675
676
677 Strain fitness (log2 ratio) -5
-4
-3
-2
-1
0
1
2
3
4
5
6 at 674.390 kb on - strand at 674.458 kb on + strand at 674.524 kb on + strand at 674.527 kb on + strand at 674.528 kb on - strand at 674.546 kb on + strand at 674.552 kb on - strand at 674.593 kb on + strand at 674.596 kb on - strand at 674.628 kb on - strand at 674.650 kb on - strand at 674.682 kb on + strand at 674.683 kb on - strand at 674.695 kb on - strand at 674.710 kb on - strand at 674.746 kb on + strand, within HMPREF1058_RS10420 at 674.839 kb on + strand, within HMPREF1058_RS10420 at 674.839 kb on + strand, within HMPREF1058_RS10420 at 674.840 kb on - strand, within HMPREF1058_RS10420 at 674.859 kb on + strand, within HMPREF1058_RS10420 at 674.885 kb on + strand, within HMPREF1058_RS10420 at 674.885 kb on + strand, within HMPREF1058_RS10420 at 674.886 kb on - strand, within HMPREF1058_RS10420 at 674.979 kb on - strand at 674.998 kb on + strand at 675.019 kb on - strand at 675.022 kb on - strand at 675.024 kb on + strand at 675.207 kb on + strand, within HMPREF1058_RS10415 at 675.244 kb on - strand, within HMPREF1058_RS10415 at 675.326 kb on + strand, within HMPREF1058_RS10415 at 675.326 kb on + strand, within HMPREF1058_RS10415 at 675.326 kb on + strand, within HMPREF1058_RS10415 at 675.382 kb on + strand at 675.382 kb on + strand at 675.382 kb on + strand at 675.383 kb on - strand at 675.387 kb on + strand at 675.405 kb on - strand at 675.417 kb on - strand at 675.435 kb on + strand at 675.436 kb on - strand at 675.463 kb on + strand at 675.464 kb on - strand at 675.474 kb on + strand, within HMPREF1058_RS10410 at 675.523 kb on + strand, within HMPREF1058_RS10410 at 675.528 kb on - strand, within HMPREF1058_RS10410 at 675.675 kb on - strand, within HMPREF1058_RS10410 at 675.675 kb on - strand, within HMPREF1058_RS10410 at 675.680 kb on + strand, within HMPREF1058_RS10410 at 675.680 kb on + strand, within HMPREF1058_RS10410 at 675.758 kb on - strand, within HMPREF1058_RS10410 at 675.785 kb on + strand, within HMPREF1058_RS10410 at 675.855 kb on + strand, within HMPREF1058_RS10410 at 675.887 kb on + strand, within HMPREF1058_RS10410 at 675.888 kb on - strand, within HMPREF1058_RS10410 at 675.955 kb on + strand, within HMPREF1058_RS10410 at 675.986 kb on + strand, within HMPREF1058_RS10410 at 675.987 kb on - strand, within HMPREF1058_RS10410 at 675.987 kb on - strand, within HMPREF1058_RS10410 at 675.987 kb on - strand, within HMPREF1058_RS10410 at 675.987 kb on - strand, within HMPREF1058_RS10410 at 675.987 kb on - strand, within HMPREF1058_RS10410 at 676.005 kb on + strand, within HMPREF1058_RS10410 at 676.009 kb on + strand, within HMPREF1058_RS10410 at 676.009 kb on + strand, within HMPREF1058_RS10410 at 676.010 kb on - strand, within HMPREF1058_RS10410 at 676.010 kb on - strand, within HMPREF1058_RS10410 at 676.010 kb on - strand, within HMPREF1058_RS10410 at 676.010 kb on - strand, within HMPREF1058_RS10410 at 676.061 kb on - strand, within HMPREF1058_RS10410 at 676.093 kb on + strand, within HMPREF1058_RS10410 at 676.107 kb on - strand, within HMPREF1058_RS10410 at 676.121 kb on - strand, within HMPREF1058_RS10410 at 676.132 kb on + strand, within HMPREF1058_RS10410 at 676.170 kb on + strand, within HMPREF1058_RS10410 at 676.217 kb on + strand, within HMPREF1058_RS10410 at 676.217 kb on + strand, within HMPREF1058_RS10410 at 676.218 kb on - strand, within HMPREF1058_RS10410 at 676.274 kb on + strand, within HMPREF1058_RS10410 at 676.274 kb on + strand, within HMPREF1058_RS10410 at 676.275 kb on - strand, within HMPREF1058_RS10410 at 676.397 kb on + strand at 676.408 kb on + strand at 676.408 kb on + strand at 676.465 kb on + strand at 676.466 kb on - strand at 676.466 kb on - strand at 676.466 kb on - strand at 676.504 kb on - strand at 676.653 kb on - strand at 676.813 kb on + strand at 676.814 kb on - strand at 676.847 kb on - strand at 676.847 kb on - strand at 676.862 kb on - strand, within HMPREF1058_RS10405 at 676.863 kb on + strand, within HMPREF1058_RS10405 at 676.886 kb on - strand, within HMPREF1058_RS10405 at 676.987 kb on + strand, within HMPREF1058_RS10405 at 676.999 kb on - strand, within HMPREF1058_RS10405 at 677.013 kb on + strand, within HMPREF1058_RS10405 at 677.038 kb on - strand, within HMPREF1058_RS10405 at 677.038 kb on - strand, within HMPREF1058_RS10405 at 677.039 kb on + strand, within HMPREF1058_RS10405 at 677.040 kb on - strand, within HMPREF1058_RS10405 at 677.045 kb on - strand, within HMPREF1058_RS10405 at 677.079 kb on - strand, within HMPREF1058_RS10405 at 677.145 kb on - strand, within HMPREF1058_RS10405 at 677.190 kb on + strand, within HMPREF1058_RS10405 at 677.190 kb on + strand, within HMPREF1058_RS10405 at 677.196 kb on - strand, within HMPREF1058_RS10405 at 677.196 kb on - strand, within HMPREF1058_RS10405 at 677.242 kb on + strand, within HMPREF1058_RS10405 at 677.250 kb on + strand, within HMPREF1058_RS10405 at 677.294 kb on + strand, within HMPREF1058_RS10405 at 677.294 kb on + strand, within HMPREF1058_RS10405 at 677.381 kb on + strand, within HMPREF1058_RS10405 at 677.381 kb on + strand, within HMPREF1058_RS10405 at 677.382 kb on - strand, within HMPREF1058_RS10405 at 677.382 kb on - strand, within HMPREF1058_RS10405 at 677.382 kb on - strand, within HMPREF1058_RS10405 at 677.385 kb on + strand, within HMPREF1058_RS10405 at 677.386 kb on - strand, within HMPREF1058_RS10405 at 677.386 kb on - strand, within HMPREF1058_RS10405 at 677.386 kb on - strand, within HMPREF1058_RS10405 at 677.407 kb on + strand, within HMPREF1058_RS10405 at 677.407 kb on + strand, within HMPREF1058_RS10405 at 677.408 kb on - strand, within HMPREF1058_RS10405
Per-strain Table
Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=MixComm; mouse2; day6 remove 674,390 - -1.5 674,458 + -0.6 674,524 + +1.2 674,527 + +0.4 674,528 - +1.0 674,546 + -0.5 674,552 - -1.8 674,593 + +0.0 674,596 - -0.4 674,628 - +1.1 674,650 - -4.0 674,682 + +0.5 674,683 - +1.0 674,695 - +0.1 674,710 - -2.7 674,746 + HMPREF1058_RS10420 0.16 +0.2 674,839 + HMPREF1058_RS10420 0.45 +2.1 674,839 + HMPREF1058_RS10420 0.45 +0.9 674,840 - HMPREF1058_RS10420 0.46 +2.8 674,859 + HMPREF1058_RS10420 0.52 +1.3 674,885 + HMPREF1058_RS10420 0.60 +0.7 674,885 + HMPREF1058_RS10420 0.60 +1.9 674,886 - HMPREF1058_RS10420 0.60 -0.7 674,979 - +0.2 674,998 + -4.7 675,019 - +1.6 675,022 - +2.2 675,024 + -1.3 675,207 + HMPREF1058_RS10415 0.52 +0.7 675,244 - HMPREF1058_RS10415 0.62 -1.2 675,326 + HMPREF1058_RS10415 0.84 +0.5 675,326 + HMPREF1058_RS10415 0.84 -0.0 675,326 + HMPREF1058_RS10415 0.84 +1.8 675,382 + +0.7 675,382 + +0.8 675,382 + +1.1 675,383 - -1.0 675,387 + +0.6 675,405 - +0.0 675,417 - -0.9 675,435 + +1.1 675,436 - -0.4 675,463 + +1.1 675,464 - -1.7 675,474 + HMPREF1058_RS10410 0.10 +0.5 675,523 + HMPREF1058_RS10410 0.15 -0.0 675,528 - HMPREF1058_RS10410 0.15 -1.2 675,675 - HMPREF1058_RS10410 0.29 +0.1 675,675 - HMPREF1058_RS10410 0.29 -1.1 675,680 + HMPREF1058_RS10410 0.30 +6.1 675,680 + HMPREF1058_RS10410 0.30 -0.5 675,758 - HMPREF1058_RS10410 0.37 -1.1 675,785 + HMPREF1058_RS10410 0.40 +1.2 675,855 + HMPREF1058_RS10410 0.47 -0.1 675,887 + HMPREF1058_RS10410 0.50 +1.6 675,888 - HMPREF1058_RS10410 0.50 -1.5 675,955 + HMPREF1058_RS10410 0.56 +0.9 675,986 + HMPREF1058_RS10410 0.59 +1.2 675,987 - HMPREF1058_RS10410 0.59 -1.0 675,987 - HMPREF1058_RS10410 0.59 +0.6 675,987 - HMPREF1058_RS10410 0.59 -1.1 675,987 - HMPREF1058_RS10410 0.59 +1.3 675,987 - HMPREF1058_RS10410 0.59 -0.7 676,005 + HMPREF1058_RS10410 0.61 -1.4 676,009 + HMPREF1058_RS10410 0.62 +0.8 676,009 + HMPREF1058_RS10410 0.62 -0.1 676,010 - HMPREF1058_RS10410 0.62 +0.5 676,010 - HMPREF1058_RS10410 0.62 +0.1 676,010 - HMPREF1058_RS10410 0.62 -0.6 676,010 - HMPREF1058_RS10410 0.62 +0.9 676,061 - HMPREF1058_RS10410 0.67 +0.2 676,093 + HMPREF1058_RS10410 0.70 -0.9 676,107 - HMPREF1058_RS10410 0.71 +1.3 676,121 - HMPREF1058_RS10410 0.72 -2.5 676,132 + HMPREF1058_RS10410 0.73 -2.1 676,170 + HMPREF1058_RS10410 0.77 -1.0 676,217 + HMPREF1058_RS10410 0.82 -0.9 676,217 + HMPREF1058_RS10410 0.82 +1.2 676,218 - HMPREF1058_RS10410 0.82 -2.5 676,274 + HMPREF1058_RS10410 0.87 +3.2 676,274 + HMPREF1058_RS10410 0.87 +0.4 676,275 - HMPREF1058_RS10410 0.87 -0.7 676,397 + -0.9 676,408 + +5.1 676,408 + -1.1 676,465 + +0.9 676,466 - -2.1 676,466 - -1.0 676,466 - +3.3 676,504 - -1.1 676,653 - -0.1 676,813 + -2.7 676,814 - +1.9 676,847 - +0.3 676,847 - +0.6 676,862 - HMPREF1058_RS10405 0.11 +0.4 676,863 + HMPREF1058_RS10405 0.11 +1.1 676,886 - HMPREF1058_RS10405 0.13 +1.9 676,987 + HMPREF1058_RS10405 0.20 -3.1 676,999 - HMPREF1058_RS10405 0.21 -0.4 677,013 + HMPREF1058_RS10405 0.21 +0.3 677,038 - HMPREF1058_RS10405 0.23 -2.1 677,038 - HMPREF1058_RS10405 0.23 +3.3 677,039 + HMPREF1058_RS10405 0.23 +2.9 677,040 - HMPREF1058_RS10405 0.23 -4.3 677,045 - HMPREF1058_RS10405 0.24 -0.1 677,079 - HMPREF1058_RS10405 0.26 +0.5 677,145 - HMPREF1058_RS10405 0.31 +0.8 677,190 + HMPREF1058_RS10405 0.34 -0.6 677,190 + HMPREF1058_RS10405 0.34 -5.7 677,196 - HMPREF1058_RS10405 0.34 -0.4 677,196 - HMPREF1058_RS10405 0.34 +0.5 677,242 + HMPREF1058_RS10405 0.38 +2.2 677,250 + HMPREF1058_RS10405 0.38 -1.1 677,294 + HMPREF1058_RS10405 0.41 -2.1 677,294 + HMPREF1058_RS10405 0.41 +0.4 677,381 + HMPREF1058_RS10405 0.47 +0.7 677,381 + HMPREF1058_RS10405 0.47 -2.7 677,382 - HMPREF1058_RS10405 0.47 +4.4 677,382 - HMPREF1058_RS10405 0.47 -1.7 677,382 - HMPREF1058_RS10405 0.47 -3.1 677,385 + HMPREF1058_RS10405 0.48 -1.1 677,386 - HMPREF1058_RS10405 0.48 +2.8 677,386 - HMPREF1058_RS10405 0.48 -0.1 677,386 - HMPREF1058_RS10405 0.48 -0.3 677,407 + HMPREF1058_RS10405 0.49 -1.4 677,407 + HMPREF1058_RS10405 0.49 +1.4 677,408 - HMPREF1058_RS10405 0.49 +0.4
Or see this region's nucleotide sequence