Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; 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_RS16700 and HMPREF1078_RS16705 are separated by 97 nucleotides HMPREF1078_RS16705 and HMPREF1078_RS16710 are separated by 29 nucleotides HMPREF1078_RS16710 and HMPREF1078_RS16715 are separated by 68 nucleotides HMPREF1078_RS16715 and HMPREF1078_RS16720 are separated by 90 nucleotides
HMPREF1078_RS16700: HMPREF1078_RS16700 - PatB family C-S lyase, at 54,879 to 56,054
_RS16700
HMPREF1078_RS16705: HMPREF1078_RS16705 - FKBP-type peptidyl-prolyl cis-trans isomerase, at 56,152 to 56,730
_RS16705
HMPREF1078_RS16710: HMPREF1078_RS16710 - chorismate synthase, at 56,760 to 57,830
_RS16710
HMPREF1078_RS16715: HMPREF1078_RS16715 - 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH, at 57,899 to 58,372
_RS16715
HMPREF1078_RS16720: HMPREF1078_RS16720 - DUF4783 domain-containing protein, at 58,463 to 58,834
_RS16720
Position (kb) 56
57
58 Strain fitness (log2 ratio) -4
-3
-2
-1
0
1
2
3 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.764 kb on + strand, within HMPREF1078_RS16700 at 55.765 kb on - strand, within HMPREF1078_RS16700 at 55.765 kb on - strand, within HMPREF1078_RS16700 at 55.765 kb on - strand, within HMPREF1078_RS16700 at 55.765 kb on - strand, within HMPREF1078_RS16700 at 55.765 kb on - strand, within HMPREF1078_RS16700 at 55.767 kb on - strand, within HMPREF1078_RS16700 at 55.798 kb on - strand, within HMPREF1078_RS16700 at 55.856 kb on - strand, within HMPREF1078_RS16700 at 55.900 kb on + strand, within HMPREF1078_RS16700 at 55.901 kb on - strand, within HMPREF1078_RS16700 at 55.917 kb on - strand, within HMPREF1078_RS16700 at 55.974 kb on - strand at 55.974 kb on - strand at 56.045 kb on + strand at 56.111 kb on + strand at 56.128 kb on + strand at 56.137 kb on + strand at 56.169 kb on + strand at 56.169 kb on + strand at 56.184 kb on + strand at 56.188 kb on + strand at 56.188 kb on + strand at 56.258 kb on - strand, within HMPREF1078_RS16705 at 56.321 kb on + strand, within HMPREF1078_RS16705 at 56.334 kb on + strand, within HMPREF1078_RS16705 at 56.362 kb on + strand, within HMPREF1078_RS16705 at 56.371 kb on + strand, within HMPREF1078_RS16705 at 56.371 kb on + strand, within HMPREF1078_RS16705 at 56.371 kb on + strand, within HMPREF1078_RS16705 at 56.387 kb on + strand, within HMPREF1078_RS16705 at 56.388 kb on - strand, within HMPREF1078_RS16705 at 56.418 kb on - strand, within HMPREF1078_RS16705 at 56.490 kb on + strand, within HMPREF1078_RS16705 at 56.513 kb on + strand, within HMPREF1078_RS16705 at 56.513 kb on + strand, within HMPREF1078_RS16705 at 56.753 kb on - strand at 56.765 kb on + strand at 56.765 kb on + strand at 56.766 kb on - strand at 56.780 kb on - strand at 56.781 kb on + strand at 56.781 kb on + strand at 56.782 kb on - strand at 56.830 kb on + strand at 56.831 kb on - strand at 56.831 kb on - strand at 56.834 kb on - strand at 56.860 kb on + strand at 56.860 kb on + strand at 56.861 kb on - strand at 56.864 kb on + strand at 56.865 kb on - strand at 56.873 kb on + strand, within HMPREF1078_RS16710 at 56.873 kb on + strand, within HMPREF1078_RS16710 at 56.947 kb on + strand, within HMPREF1078_RS16710 at 56.963 kb on + strand, within HMPREF1078_RS16710 at 56.967 kb on + strand, within HMPREF1078_RS16710 at 56.967 kb on + strand, within HMPREF1078_RS16710 at 56.968 kb on - strand, within HMPREF1078_RS16710 at 56.968 kb on - strand, within HMPREF1078_RS16710 at 57.036 kb on + strand, within HMPREF1078_RS16710 at 57.036 kb on + strand, within HMPREF1078_RS16710 at 57.041 kb on + strand, within HMPREF1078_RS16710 at 57.044 kb on + strand, within HMPREF1078_RS16710 at 57.044 kb on + strand, within HMPREF1078_RS16710 at 57.044 kb on + strand, within HMPREF1078_RS16710 at 57.044 kb on + strand, within HMPREF1078_RS16710 at 57.044 kb on + strand, within HMPREF1078_RS16710 at 57.057 kb on + strand, within HMPREF1078_RS16710 at 57.079 kb on + strand, within HMPREF1078_RS16710 at 57.079 kb on - strand, within HMPREF1078_RS16710 at 57.097 kb on - strand, within HMPREF1078_RS16710 at 57.097 kb on - strand, within HMPREF1078_RS16710 at 57.208 kb on + strand, within HMPREF1078_RS16710 at 57.209 kb on - strand, within HMPREF1078_RS16710 at 57.255 kb on + strand, within HMPREF1078_RS16710 at 57.264 kb on + strand, within HMPREF1078_RS16710 at 57.296 kb on - strand, within HMPREF1078_RS16710 at 57.366 kb on - strand, within HMPREF1078_RS16710 at 57.428 kb on - strand, within HMPREF1078_RS16710 at 57.495 kb on + strand, within HMPREF1078_RS16710 at 57.521 kb on - strand, within HMPREF1078_RS16710 at 57.522 kb on + strand, within HMPREF1078_RS16710 at 57.581 kb on + strand, within HMPREF1078_RS16710 at 57.601 kb on + strand, within HMPREF1078_RS16710 at 57.602 kb on - strand, within HMPREF1078_RS16710 at 57.611 kb on + strand, within HMPREF1078_RS16710 at 57.611 kb on + strand, within HMPREF1078_RS16710 at 57.629 kb on + strand, within HMPREF1078_RS16710 at 57.633 kb on + strand, within HMPREF1078_RS16710 at 57.633 kb on + strand, within HMPREF1078_RS16710 at 57.633 kb on + strand, within HMPREF1078_RS16710 at 57.634 kb on - strand, within HMPREF1078_RS16710 at 57.693 kb on - strand, within HMPREF1078_RS16710 at 57.809 kb on + strand at 57.810 kb on - strand at 57.849 kb on + strand at 57.850 kb on - strand at 57.850 kb on - strand at 57.855 kb on + strand at 57.856 kb on - strand at 57.866 kb on + strand at 57.867 kb on - strand at 57.876 kb on + strand at 57.882 kb on + strand at 57.882 kb on + strand at 57.900 kb on + strand at 57.900 kb on + strand at 57.901 kb on - strand at 57.901 kb on - strand at 57.913 kb on - strand at 57.946 kb on - strand at 57.946 kb on - strand at 58.090 kb on + strand, within HMPREF1078_RS16715 at 58.091 kb on - strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.110 kb on + strand, within HMPREF1078_RS16715 at 58.111 kb on - strand, within HMPREF1078_RS16715 at 58.111 kb on - strand, within HMPREF1078_RS16715 at 58.167 kb on + strand, within HMPREF1078_RS16715 at 58.167 kb on + strand, within HMPREF1078_RS16715 at 58.182 kb on - strand, within HMPREF1078_RS16715 at 58.250 kb on - strand, within HMPREF1078_RS16715 at 58.282 kb on + strand, within HMPREF1078_RS16715 at 58.283 kb on - strand, within HMPREF1078_RS16715 at 58.303 kb on + strand, within HMPREF1078_RS16715 at 58.303 kb on + strand, within HMPREF1078_RS16715 at 58.304 kb on - strand, within HMPREF1078_RS16715 at 58.304 kb on - strand, within HMPREF1078_RS16715 at 58.305 kb on + strand, within HMPREF1078_RS16715 at 58.306 kb on - strand, within HMPREF1078_RS16715 at 58.402 kb on - strand at 58.422 kb on + strand at 58.422 kb on + strand at 58.422 kb on + strand at 58.430 kb on + strand at 58.435 kb on + strand at 58.438 kb on + strand at 58.512 kb on + strand, within HMPREF1078_RS16720 at 58.512 kb on + strand, within HMPREF1078_RS16720 at 58.527 kb on + strand, within HMPREF1078_RS16720 at 58.534 kb on + strand, within HMPREF1078_RS16720 at 58.592 kb on + strand, within HMPREF1078_RS16720 at 58.746 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.750 kb on + strand, within HMPREF1078_RS16720 at 58.784 kb on + strand, within HMPREF1078_RS16720 at 58.784 kb on + strand, within HMPREF1078_RS16720 at 58.810 kb on + strand at 58.812 kb on + strand at 58.812 kb on + strand at 58.812 kb on + strand
Per-strain Table
Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=Mono; mouse17; day3 remove 55,764 + HMPREF1078_RS16700 0.75 +0.7 55,764 + HMPREF1078_RS16700 0.75 -0.6 55,764 + HMPREF1078_RS16700 0.75 -2.0 55,764 + HMPREF1078_RS16700 0.75 -1.0 55,764 + HMPREF1078_RS16700 0.75 -2.8 55,764 + HMPREF1078_RS16700 0.75 +0.3 55,764 + HMPREF1078_RS16700 0.75 +1.2 55,765 - HMPREF1078_RS16700 0.75 -2.9 55,765 - HMPREF1078_RS16700 0.75 -1.5 55,765 - HMPREF1078_RS16700 0.75 -0.2 55,765 - HMPREF1078_RS16700 0.75 -0.7 55,765 - HMPREF1078_RS16700 0.75 -0.6 55,767 - HMPREF1078_RS16700 0.76 +1.1 55,798 - HMPREF1078_RS16700 0.78 +1.0 55,856 - HMPREF1078_RS16700 0.83 -1.9 55,900 + HMPREF1078_RS16700 0.87 -2.5 55,901 - HMPREF1078_RS16700 0.87 -0.0 55,917 - HMPREF1078_RS16700 0.88 -1.0 55,974 - -0.5 55,974 - +1.0 56,045 + -0.6 56,111 + +0.5 56,128 + +0.2 56,137 + -0.4 56,169 + -1.4 56,169 + +1.0 56,184 + +1.0 56,188 + +1.6 56,188 + -1.7 56,258 - HMPREF1078_RS16705 0.18 -0.0 56,321 + HMPREF1078_RS16705 0.29 +0.6 56,334 + HMPREF1078_RS16705 0.31 -0.8 56,362 + HMPREF1078_RS16705 0.36 -0.6 56,371 + HMPREF1078_RS16705 0.38 -2.6 56,371 + HMPREF1078_RS16705 0.38 +1.0 56,371 + HMPREF1078_RS16705 0.38 +1.0 56,387 + HMPREF1078_RS16705 0.41 -1.0 56,388 - HMPREF1078_RS16705 0.41 -0.0 56,418 - HMPREF1078_RS16705 0.46 -0.6 56,490 + HMPREF1078_RS16705 0.58 +1.7 56,513 + HMPREF1078_RS16705 0.62 -0.9 56,513 + HMPREF1078_RS16705 0.62 +1.6 56,753 - -0.0 56,765 + -1.4 56,765 + +0.6 56,766 - -1.4 56,780 - -0.0 56,781 + -2.2 56,781 + +1.0 56,782 - -2.4 56,830 + -1.7 56,831 - -1.4 56,831 - +1.0 56,834 - -0.0 56,860 + -1.0 56,860 + -0.6 56,861 - -0.6 56,864 + -0.0 56,865 - -0.6 56,873 + HMPREF1078_RS16710 0.11 -1.0 56,873 + HMPREF1078_RS16710 0.11 -1.8 56,947 + HMPREF1078_RS16710 0.17 -1.8 56,963 + HMPREF1078_RS16710 0.19 -4.3 56,967 + HMPREF1078_RS16710 0.19 +0.2 56,967 + HMPREF1078_RS16710 0.19 -0.0 56,968 - HMPREF1078_RS16710 0.19 -0.0 56,968 - HMPREF1078_RS16710 0.19 -0.0 57,036 + HMPREF1078_RS16710 0.26 -0.0 57,036 + HMPREF1078_RS16710 0.26 -1.0 57,041 + HMPREF1078_RS16710 0.26 -0.6 57,044 + HMPREF1078_RS16710 0.27 -2.2 57,044 + HMPREF1078_RS16710 0.27 -0.6 57,044 + HMPREF1078_RS16710 0.27 -1.0 57,044 + HMPREF1078_RS16710 0.27 -0.0 57,044 + HMPREF1078_RS16710 0.27 +1.0 57,057 + HMPREF1078_RS16710 0.28 +1.0 57,079 + HMPREF1078_RS16710 0.30 -1.8 57,079 - HMPREF1078_RS16710 0.30 -1.4 57,097 - HMPREF1078_RS16710 0.31 -0.0 57,097 - HMPREF1078_RS16710 0.31 -1.6 57,208 + HMPREF1078_RS16710 0.42 -0.6 57,209 - HMPREF1078_RS16710 0.42 -1.8 57,255 + HMPREF1078_RS16710 0.46 -1.8 57,264 + HMPREF1078_RS16710 0.47 -1.6 57,296 - HMPREF1078_RS16710 0.50 -0.6 57,366 - HMPREF1078_RS16710 0.57 -1.6 57,428 - HMPREF1078_RS16710 0.62 +1.0 57,495 + HMPREF1078_RS16710 0.69 -1.6 57,521 - HMPREF1078_RS16710 0.71 -0.6 57,522 + HMPREF1078_RS16710 0.71 -2.2 57,581 + HMPREF1078_RS16710 0.77 +1.0 57,601 + HMPREF1078_RS16710 0.79 +1.0 57,602 - HMPREF1078_RS16710 0.79 +1.0 57,611 + HMPREF1078_RS16710 0.79 -1.0 57,611 + HMPREF1078_RS16710 0.79 +0.6 57,629 + HMPREF1078_RS16710 0.81 -1.6 57,633 + HMPREF1078_RS16710 0.82 -0.0 57,633 + HMPREF1078_RS16710 0.82 -0.0 57,633 + HMPREF1078_RS16710 0.82 -0.6 57,634 - HMPREF1078_RS16710 0.82 -1.0 57,693 - HMPREF1078_RS16710 0.87 -3.0 57,809 + +1.0 57,810 - -1.8 57,849 + +0.0 57,850 - +1.0 57,850 - -1.0 57,855 + -1.0 57,856 - +0.5 57,866 + +0.0 57,867 - -0.0 57,876 + +3.3 57,882 + +0.5 57,882 + +1.1 57,900 + +1.2 57,900 + +2.0 57,901 - +0.6 57,901 - -0.4 57,913 - -1.8 57,946 - -0.6 57,946 - +0.2 58,090 + HMPREF1078_RS16715 0.40 +0.6 58,091 - HMPREF1078_RS16715 0.41 -0.3 58,110 + HMPREF1078_RS16715 0.45 -0.0 58,110 + HMPREF1078_RS16715 0.45 -0.0 58,110 + HMPREF1078_RS16715 0.45 -1.2 58,110 + HMPREF1078_RS16715 0.45 +0.3 58,110 + HMPREF1078_RS16715 0.45 +1.5 58,110 + HMPREF1078_RS16715 0.45 -0.0 58,110 + HMPREF1078_RS16715 0.45 -0.2 58,110 + HMPREF1078_RS16715 0.45 -0.0 58,111 - HMPREF1078_RS16715 0.45 +1.3 58,111 - HMPREF1078_RS16715 0.45 +0.3 58,167 + HMPREF1078_RS16715 0.57 -0.3 58,167 + HMPREF1078_RS16715 0.57 -1.2 58,182 - HMPREF1078_RS16715 0.60 +0.6 58,250 - HMPREF1078_RS16715 0.74 +0.1 58,282 + HMPREF1078_RS16715 0.81 +0.4 58,283 - HMPREF1078_RS16715 0.81 +1.0 58,303 + HMPREF1078_RS16715 0.85 -1.8 58,303 + HMPREF1078_RS16715 0.85 +0.2 58,304 - HMPREF1078_RS16715 0.85 -1.7 58,304 - HMPREF1078_RS16715 0.85 -0.1 58,305 + HMPREF1078_RS16715 0.86 -1.4 58,306 - HMPREF1078_RS16715 0.86 +0.0 58,402 - -1.1 58,422 + -1.0 58,422 + -0.4 58,422 + +0.3 58,430 + -1.2 58,435 + -1.0 58,438 + +0.9 58,512 + HMPREF1078_RS16720 0.13 +2.0 58,512 + HMPREF1078_RS16720 0.13 -0.4 58,527 + HMPREF1078_RS16720 0.17 +0.8 58,534 + HMPREF1078_RS16720 0.19 +0.6 58,592 + HMPREF1078_RS16720 0.35 +0.0 58,746 + HMPREF1078_RS16720 0.76 -1.4 58,750 + HMPREF1078_RS16720 0.77 +1.0 58,750 + HMPREF1078_RS16720 0.77 -1.1 58,750 + HMPREF1078_RS16720 0.77 -0.3 58,750 + HMPREF1078_RS16720 0.77 +0.1 58,750 + HMPREF1078_RS16720 0.77 -1.7 58,750 + HMPREF1078_RS16720 0.77 +1.3 58,784 + HMPREF1078_RS16720 0.86 -0.7 58,784 + HMPREF1078_RS16720 0.86 +1.3 58,810 + -1.0 58,812 + -0.2 58,812 + +1.0 58,812 + -0.8
Or see this region's nucleotide sequence