Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; 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_RS07535 and HMPREF1078_RS07540 are separated by 340 nucleotides HMPREF1078_RS07540 and HMPREF1078_RS07545 are separated by 109 nucleotides
HMPREF1078_RS07535: HMPREF1078_RS07535 - glycyl radical protein, at 39,126 to 41,564
_RS07535
HMPREF1078_RS07540: HMPREF1078_RS07540 - sigma-54 dependent transcriptional regulator, at 41,905 to 43,269
_RS07540
HMPREF1078_RS07545: HMPREF1078_RS07545 - DUF418 domain-containing protein, at 43,379 to 44,551
_RS07545
Position (kb) 41
42
43
44 Strain fitness (log2 ratio) -5
-4
-3
-2
-1
0
1
2
3
4 at 40.965 kb on - strand, within HMPREF1078_RS07535 at 40.991 kb on - strand, within HMPREF1078_RS07535 at 40.995 kb on - strand, within HMPREF1078_RS07535 at 40.996 kb on + strand, within HMPREF1078_RS07535 at 40.997 kb on - strand, within HMPREF1078_RS07535 at 41.019 kb on - strand, within HMPREF1078_RS07535 at 41.069 kb on - strand, within HMPREF1078_RS07535 at 41.091 kb on + strand, within HMPREF1078_RS07535 at 41.105 kb on + strand, within HMPREF1078_RS07535 at 41.106 kb on - strand, within HMPREF1078_RS07535 at 41.155 kb on + strand, within HMPREF1078_RS07535 at 41.185 kb on + strand, within HMPREF1078_RS07535 at 41.315 kb on - strand, within HMPREF1078_RS07535 at 41.331 kb on - strand at 41.556 kb on + strand at 41.558 kb on + strand at 41.564 kb on + strand at 41.564 kb on + strand at 41.564 kb on + strand at 41.564 kb on + strand at 41.564 kb on + strand at 41.565 kb on - strand at 41.565 kb on - strand at 41.568 kb on - strand at 41.569 kb on + strand at 41.569 kb on + strand at 41.570 kb on - strand at 41.571 kb on + strand at 41.633 kb on + strand at 41.665 kb on + strand at 41.665 kb on + strand at 41.666 kb on - strand at 41.666 kb on - strand at 41.669 kb on - strand at 41.669 kb on - strand at 41.751 kb on - strand at 41.751 kb on - strand at 41.790 kb on - strand at 41.814 kb on + strand at 41.814 kb on + strand at 41.872 kb on - strand at 41.931 kb on + strand at 41.931 kb on + strand at 41.931 kb on + strand at 41.932 kb on - strand at 41.983 kb on - strand at 42.111 kb on + strand, within HMPREF1078_RS07540 at 42.114 kb on - strand, within HMPREF1078_RS07540 at 42.114 kb on - strand, within HMPREF1078_RS07540 at 42.135 kb on + strand, within HMPREF1078_RS07540 at 42.136 kb on - strand, within HMPREF1078_RS07540 at 42.136 kb on - strand, within HMPREF1078_RS07540 at 42.140 kb on + strand, within HMPREF1078_RS07540 at 42.140 kb on + strand, within HMPREF1078_RS07540 at 42.140 kb on + strand, within HMPREF1078_RS07540 at 42.141 kb on - strand, within HMPREF1078_RS07540 at 42.141 kb on - strand, within HMPREF1078_RS07540 at 42.186 kb on - strand, within HMPREF1078_RS07540 at 42.225 kb on + strand, within HMPREF1078_RS07540 at 42.228 kb on + strand, within HMPREF1078_RS07540 at 42.228 kb on + strand, within HMPREF1078_RS07540 at 42.228 kb on + strand, within HMPREF1078_RS07540 at 42.229 kb on - strand, within HMPREF1078_RS07540 at 42.346 kb on + strand, within HMPREF1078_RS07540 at 42.346 kb on + strand, within HMPREF1078_RS07540 at 42.347 kb on - strand, within HMPREF1078_RS07540 at 42.409 kb on - strand, within HMPREF1078_RS07540 at 42.442 kb on - strand, within HMPREF1078_RS07540 at 42.487 kb on + strand, within HMPREF1078_RS07540 at 42.487 kb on + strand, within HMPREF1078_RS07540 at 42.488 kb on - strand, within HMPREF1078_RS07540 at 42.494 kb on - strand, within HMPREF1078_RS07540 at 42.494 kb on - strand, within HMPREF1078_RS07540 at 42.494 kb on - strand, within HMPREF1078_RS07540 at 42.501 kb on - strand, within HMPREF1078_RS07540 at 42.535 kb on - strand, within HMPREF1078_RS07540 at 42.535 kb on - strand, within HMPREF1078_RS07540 at 42.568 kb on - strand, within HMPREF1078_RS07540 at 42.577 kb on - strand, within HMPREF1078_RS07540 at 42.577 kb on - strand, within HMPREF1078_RS07540 at 42.660 kb on + strand, within HMPREF1078_RS07540 at 42.675 kb on + strand, within HMPREF1078_RS07540 at 42.676 kb on - strand, within HMPREF1078_RS07540 at 42.710 kb on + strand, within HMPREF1078_RS07540 at 42.711 kb on - strand, within HMPREF1078_RS07540 at 42.724 kb on - strand, within HMPREF1078_RS07540 at 42.753 kb on + strand, within HMPREF1078_RS07540 at 42.753 kb on + strand, within HMPREF1078_RS07540 at 42.753 kb on + strand, within HMPREF1078_RS07540 at 42.753 kb on + strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.754 kb on - strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.775 kb on + strand, within HMPREF1078_RS07540 at 42.776 kb on - strand, within HMPREF1078_RS07540 at 42.776 kb on - strand, within HMPREF1078_RS07540 at 42.776 kb on - strand, within HMPREF1078_RS07540 at 42.786 kb on - strand, within HMPREF1078_RS07540 at 42.822 kb on - strand, within HMPREF1078_RS07540 at 42.822 kb on - strand, within HMPREF1078_RS07540 at 42.822 kb on - strand, within HMPREF1078_RS07540 at 42.919 kb on + strand, within HMPREF1078_RS07540 at 42.919 kb on + strand, within HMPREF1078_RS07540 at 42.941 kb on - strand, within HMPREF1078_RS07540 at 42.972 kb on + strand, within HMPREF1078_RS07540 at 42.972 kb on + strand, within HMPREF1078_RS07540 at 42.972 kb on + strand, within HMPREF1078_RS07540 at 42.973 kb on - strand, within HMPREF1078_RS07540 at 43.016 kb on - strand, within HMPREF1078_RS07540 at 43.016 kb on - strand, within HMPREF1078_RS07540 at 43.177 kb on + strand at 43.237 kb on + strand at 43.237 kb on + strand at 43.239 kb on + strand at 43.240 kb on - strand at 43.250 kb on - strand at 43.269 kb on + strand at 43.270 kb on - strand at 43.290 kb on - strand at 43.549 kb on + strand, within HMPREF1078_RS07545 at 43.560 kb on - strand, within HMPREF1078_RS07545 at 43.560 kb on - strand, within HMPREF1078_RS07545 at 43.560 kb on - strand, within HMPREF1078_RS07545 at 43.565 kb on - strand, within HMPREF1078_RS07545 at 43.579 kb on - strand, within HMPREF1078_RS07545 at 43.579 kb on - strand, within HMPREF1078_RS07545 at 43.628 kb on - strand, within HMPREF1078_RS07545 at 43.776 kb on + strand, within HMPREF1078_RS07545 at 43.776 kb on + strand, within HMPREF1078_RS07545 at 44.011 kb on + strand, within HMPREF1078_RS07545 at 44.011 kb on + strand, within HMPREF1078_RS07545 at 44.012 kb on - strand, within HMPREF1078_RS07545 at 44.012 kb on - strand, within HMPREF1078_RS07545 at 44.012 kb on - strand, within HMPREF1078_RS07545 at 44.012 kb on - strand, within HMPREF1078_RS07545 at 44.020 kb on + strand, within HMPREF1078_RS07545 at 44.052 kb on + strand, within HMPREF1078_RS07545 at 44.053 kb on - strand, within HMPREF1078_RS07545 at 44.053 kb on - strand, within HMPREF1078_RS07545 at 44.114 kb on - strand, within HMPREF1078_RS07545 at 44.177 kb on + strand, within HMPREF1078_RS07545 at 44.192 kb on + strand, within HMPREF1078_RS07545 at 44.192 kb on + strand, within HMPREF1078_RS07545 at 44.195 kb on + strand, within HMPREF1078_RS07545
Per-strain Table
Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day4 remove 40,965 - HMPREF1078_RS07535 0.75 -0.8 40,991 - HMPREF1078_RS07535 0.76 -0.3 40,995 - HMPREF1078_RS07535 0.77 -2.4 40,996 + HMPREF1078_RS07535 0.77 -1.0 40,997 - HMPREF1078_RS07535 0.77 +0.1 41,019 - HMPREF1078_RS07535 0.78 +1.5 41,069 - HMPREF1078_RS07535 0.80 -1.1 41,091 + HMPREF1078_RS07535 0.81 +2.3 41,105 + HMPREF1078_RS07535 0.81 -0.8 41,106 - HMPREF1078_RS07535 0.81 +0.9 41,155 + HMPREF1078_RS07535 0.83 +1.7 41,185 + HMPREF1078_RS07535 0.84 +1.4 41,315 - HMPREF1078_RS07535 0.90 +0.2 41,331 - -1.3 41,556 + +3.3 41,558 + -1.4 41,564 + -0.6 41,564 + -1.4 41,564 + -1.4 41,564 + +1.2 41,564 + -0.5 41,565 - -0.6 41,565 - -2.5 41,568 - -0.7 41,569 + +0.2 41,569 + +0.7 41,570 - +1.5 41,571 + +0.5 41,633 + -2.5 41,665 + +1.1 41,665 + -1.1 41,666 - +2.6 41,666 - -1.6 41,669 - -0.3 41,669 - +0.8 41,751 - -2.3 41,751 - +0.1 41,790 - +0.3 41,814 + +0.0 41,814 + +1.3 41,872 - +1.7 41,931 + -1.6 41,931 + -0.2 41,931 + +1.8 41,932 - -1.5 41,983 - +1.5 42,111 + HMPREF1078_RS07540 0.15 -2.1 42,114 - HMPREF1078_RS07540 0.15 +0.5 42,114 - HMPREF1078_RS07540 0.15 +2.1 42,135 + HMPREF1078_RS07540 0.17 +1.9 42,136 - HMPREF1078_RS07540 0.17 +2.0 42,136 - HMPREF1078_RS07540 0.17 +0.3 42,140 + HMPREF1078_RS07540 0.17 -3.4 42,140 + HMPREF1078_RS07540 0.17 +2.1 42,140 + HMPREF1078_RS07540 0.17 +0.3 42,141 - HMPREF1078_RS07540 0.17 +0.2 42,141 - HMPREF1078_RS07540 0.17 -2.7 42,186 - HMPREF1078_RS07540 0.21 +1.4 42,225 + HMPREF1078_RS07540 0.23 -0.2 42,228 + HMPREF1078_RS07540 0.24 -1.0 42,228 + HMPREF1078_RS07540 0.24 +0.1 42,228 + HMPREF1078_RS07540 0.24 -0.4 42,229 - HMPREF1078_RS07540 0.24 -0.3 42,346 + HMPREF1078_RS07540 0.32 +1.2 42,346 + HMPREF1078_RS07540 0.32 -1.0 42,347 - HMPREF1078_RS07540 0.32 +0.3 42,409 - HMPREF1078_RS07540 0.37 -1.9 42,442 - HMPREF1078_RS07540 0.39 +1.0 42,487 + HMPREF1078_RS07540 0.43 +2.3 42,487 + HMPREF1078_RS07540 0.43 -2.3 42,488 - HMPREF1078_RS07540 0.43 -2.3 42,494 - HMPREF1078_RS07540 0.43 -2.8 42,494 - HMPREF1078_RS07540 0.43 -2.2 42,494 - HMPREF1078_RS07540 0.43 -1.3 42,501 - HMPREF1078_RS07540 0.44 -2.1 42,535 - HMPREF1078_RS07540 0.46 -0.3 42,535 - HMPREF1078_RS07540 0.46 +1.9 42,568 - HMPREF1078_RS07540 0.49 +2.2 42,577 - HMPREF1078_RS07540 0.49 +0.7 42,577 - HMPREF1078_RS07540 0.49 -0.2 42,660 + HMPREF1078_RS07540 0.55 +1.0 42,675 + HMPREF1078_RS07540 0.56 +1.2 42,676 - HMPREF1078_RS07540 0.56 -0.2 42,710 + HMPREF1078_RS07540 0.59 +3.7 42,711 - HMPREF1078_RS07540 0.59 +0.5 42,724 - HMPREF1078_RS07540 0.60 -2.2 42,753 + HMPREF1078_RS07540 0.62 -1.3 42,753 + HMPREF1078_RS07540 0.62 -2.4 42,753 + HMPREF1078_RS07540 0.62 -1.3 42,753 + HMPREF1078_RS07540 0.62 -1.6 42,754 - HMPREF1078_RS07540 0.62 -0.4 42,754 - HMPREF1078_RS07540 0.62 -1.7 42,754 - HMPREF1078_RS07540 0.62 +2.5 42,754 - HMPREF1078_RS07540 0.62 +0.4 42,754 - HMPREF1078_RS07540 0.62 +0.9 42,754 - HMPREF1078_RS07540 0.62 -1.1 42,775 + HMPREF1078_RS07540 0.64 -2.4 42,775 + HMPREF1078_RS07540 0.64 -1.4 42,775 + HMPREF1078_RS07540 0.64 -0.8 42,775 + HMPREF1078_RS07540 0.64 -1.9 42,775 + HMPREF1078_RS07540 0.64 -0.5 42,775 + HMPREF1078_RS07540 0.64 -4.9 42,775 + HMPREF1078_RS07540 0.64 -0.6 42,776 - HMPREF1078_RS07540 0.64 -2.7 42,776 - HMPREF1078_RS07540 0.64 -4.2 42,776 - HMPREF1078_RS07540 0.64 -0.7 42,786 - HMPREF1078_RS07540 0.65 +0.6 42,822 - HMPREF1078_RS07540 0.67 -2.0 42,822 - HMPREF1078_RS07540 0.67 +0.4 42,822 - HMPREF1078_RS07540 0.67 +0.3 42,919 + HMPREF1078_RS07540 0.74 -0.3 42,919 + HMPREF1078_RS07540 0.74 +2.0 42,941 - HMPREF1078_RS07540 0.76 -1.0 42,972 + HMPREF1078_RS07540 0.78 -0.7 42,972 + HMPREF1078_RS07540 0.78 +3.7 42,972 + HMPREF1078_RS07540 0.78 -2.2 42,973 - HMPREF1078_RS07540 0.78 +0.1 43,016 - HMPREF1078_RS07540 0.81 +0.5 43,016 - HMPREF1078_RS07540 0.81 +1.6 43,177 + +0.8 43,237 + +1.3 43,237 + -2.8 43,239 + -0.3 43,240 - +0.6 43,250 - -1.5 43,269 + +4.6 43,270 - -0.6 43,290 - -3.3 43,549 + HMPREF1078_RS07545 0.14 -3.2 43,560 - HMPREF1078_RS07545 0.15 +0.5 43,560 - HMPREF1078_RS07545 0.15 -1.4 43,560 - HMPREF1078_RS07545 0.15 +0.3 43,565 - HMPREF1078_RS07545 0.16 +1.3 43,579 - HMPREF1078_RS07545 0.17 +1.0 43,579 - HMPREF1078_RS07545 0.17 -2.2 43,628 - HMPREF1078_RS07545 0.21 -0.4 43,776 + HMPREF1078_RS07545 0.34 -1.6 43,776 + HMPREF1078_RS07545 0.34 +0.7 44,011 + HMPREF1078_RS07545 0.54 -3.3 44,011 + HMPREF1078_RS07545 0.54 -3.3 44,012 - HMPREF1078_RS07545 0.54 +3.8 44,012 - HMPREF1078_RS07545 0.54 +0.3 44,012 - HMPREF1078_RS07545 0.54 -0.8 44,012 - HMPREF1078_RS07545 0.54 -2.7 44,020 + HMPREF1078_RS07545 0.55 -1.9 44,052 + HMPREF1078_RS07545 0.57 +2.4 44,053 - HMPREF1078_RS07545 0.57 -1.2 44,053 - HMPREF1078_RS07545 0.57 -3.2 44,114 - HMPREF1078_RS07545 0.63 -0.9 44,177 + HMPREF1078_RS07545 0.68 +1.9 44,192 + HMPREF1078_RS07545 0.69 -0.3 44,192 + HMPREF1078_RS07545 0.69 -1.7 44,195 + HMPREF1078_RS07545 0.70 -0.2
Or see this region's nucleotide sequence