Experiment: diet=StandardDiet; sample=FecalPellet; inoculation=MixComm; mouse2; day5
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_RS05695 and HMPREF1058_RS05690 are separated by 142 nucleotides HMPREF1058_RS05690 and HMPREF1058_RS20935 are separated by 374 nucleotides HMPREF1058_RS20935 and HMPREF1058_RS05675 are separated by 137 nucleotides
HMPREF1058_RS05695: HMPREF1058_RS05695 - helix-turn-helix domain-containing protein, at 103,399 to 103,719
_RS05695
HMPREF1058_RS05690: HMPREF1058_RS05690 - hypothetical protein, at 103,862 to 104,137
_RS05690
HMPREF1058_RS20935: HMPREF1058_RS20935 - helix-turn-helix domain-containing protein, at 104,512 to 105,448
_RS20935
HMPREF1058_RS05675: HMPREF1058_RS05675 - site-specific integrase, at 105,586 to 106,458
_RS05675
Position (kb) 104
105
106 Strain fitness (log2 ratio) -3
-2
-1
0
1
2 at 103.512 kb on - strand, within HMPREF1058_RS05695 at 103.645 kb on - strand, within HMPREF1058_RS05695 at 103.707 kb on + strand at 103.733 kb on - strand at 103.737 kb on + strand at 103.762 kb on - strand at 103.765 kb on + strand at 103.807 kb on - strand at 103.810 kb on - strand at 103.822 kb on + strand at 103.859 kb on - strand at 103.860 kb on - strand at 103.903 kb on + strand, within HMPREF1058_RS05690 at 103.903 kb on + strand, within HMPREF1058_RS05690 at 103.964 kb on - strand, within HMPREF1058_RS05690 at 103.987 kb on + strand, within HMPREF1058_RS05690 at 104.156 kb on + strand at 104.204 kb on - strand at 104.447 kb on + strand at 104.471 kb on + strand at 104.471 kb on + strand at 104.474 kb on - strand at 104.670 kb on - strand, within HMPREF1058_RS20935 at 104.683 kb on + strand, within HMPREF1058_RS20935 at 104.708 kb on + strand, within HMPREF1058_RS20935 at 104.731 kb on + strand, within HMPREF1058_RS20935 at 104.732 kb on - strand, within HMPREF1058_RS20935 at 104.737 kb on + strand, within HMPREF1058_RS20935 at 104.775 kb on + strand, within HMPREF1058_RS20935 at 104.775 kb on + strand, within HMPREF1058_RS20935 at 104.933 kb on + strand, within HMPREF1058_RS20935 at 105.002 kb on + strand, within HMPREF1058_RS20935 at 105.059 kb on + strand, within HMPREF1058_RS20935 at 105.099 kb on + strand, within HMPREF1058_RS20935 at 105.100 kb on - strand, within HMPREF1058_RS20935 at 105.100 kb on - strand, within HMPREF1058_RS20935 at 105.100 kb on - strand, within HMPREF1058_RS20935 at 105.104 kb on - strand, within HMPREF1058_RS20935 at 105.230 kb on + strand, within HMPREF1058_RS20935 at 105.230 kb on + strand, within HMPREF1058_RS20935 at 105.231 kb on - strand, within HMPREF1058_RS20935 at 105.231 kb on - strand, within HMPREF1058_RS20935 at 105.385 kb on - strand at 105.478 kb on - strand at 105.478 kb on - strand at 105.502 kb on + strand at 105.627 kb on + strand at 105.651 kb on - strand at 105.688 kb on - strand, within HMPREF1058_RS05675 at 105.795 kb on - strand, within HMPREF1058_RS05675 at 105.804 kb on + strand, within HMPREF1058_RS05675 at 105.805 kb on - strand, within HMPREF1058_RS05675 at 105.928 kb on + strand, within HMPREF1058_RS05675 at 105.951 kb on - strand, within HMPREF1058_RS05675 at 106.009 kb on + strand, within HMPREF1058_RS05675 at 106.010 kb on - strand, within HMPREF1058_RS05675 at 106.056 kb on + strand, within HMPREF1058_RS05675 at 106.327 kb on + strand, within HMPREF1058_RS05675 at 106.327 kb on + strand, within HMPREF1058_RS05675
Per-strain Table
Position Strand Gene LocusTag Fraction diet=StandardDiet; sample=FecalPellet; inoculation=MixComm; mouse2; day5 remove 103,512 - HMPREF1058_RS05695 0.35 +1.9 103,645 - HMPREF1058_RS05695 0.77 -0.9 103,707 + -0.4 103,733 - +1.5 103,737 + -1.0 103,762 - +0.3 103,765 + +1.3 103,807 - -1.5 103,810 - -1.6 103,822 + -0.1 103,859 - +0.1 103,860 - +1.1 103,903 + HMPREF1058_RS05690 0.15 +0.0 103,903 + HMPREF1058_RS05690 0.15 -0.4 103,964 - HMPREF1058_RS05690 0.37 +1.2 103,987 + HMPREF1058_RS05690 0.45 -0.8 104,156 + -0.4 104,204 - -2.3 104,447 + -2.0 104,471 + -0.2 104,471 + +1.6 104,474 - +1.3 104,670 - HMPREF1058_RS20935 0.17 +2.3 104,683 + HMPREF1058_RS20935 0.18 -2.3 104,708 + HMPREF1058_RS20935 0.21 -2.6 104,731 + HMPREF1058_RS20935 0.23 -3.7 104,732 - HMPREF1058_RS20935 0.23 +1.2 104,737 + HMPREF1058_RS20935 0.24 -1.0 104,775 + HMPREF1058_RS20935 0.28 +1.0 104,775 + HMPREF1058_RS20935 0.28 +0.0 104,933 + HMPREF1058_RS20935 0.45 -3.7 105,002 + HMPREF1058_RS20935 0.52 +1.1 105,059 + HMPREF1058_RS20935 0.58 -1.3 105,099 + HMPREF1058_RS20935 0.63 -0.9 105,100 - HMPREF1058_RS20935 0.63 -1.1 105,100 - HMPREF1058_RS20935 0.63 -1.3 105,100 - HMPREF1058_RS20935 0.63 -2.8 105,104 - HMPREF1058_RS20935 0.63 -0.1 105,230 + HMPREF1058_RS20935 0.77 +0.0 105,230 + HMPREF1058_RS20935 0.77 -1.1 105,231 - HMPREF1058_RS20935 0.77 +1.7 105,231 - HMPREF1058_RS20935 0.77 -1.0 105,385 - -2.0 105,478 - -1.0 105,478 - +0.7 105,502 + -0.3 105,627 + -1.0 105,651 - -3.0 105,688 - HMPREF1058_RS05675 0.12 +0.0 105,795 - HMPREF1058_RS05675 0.24 +0.0 105,804 + HMPREF1058_RS05675 0.25 -1.0 105,805 - HMPREF1058_RS05675 0.25 -2.2 105,928 + HMPREF1058_RS05675 0.39 +0.7 105,951 - HMPREF1058_RS05675 0.42 +1.0 106,009 + HMPREF1058_RS05675 0.48 -1.3 106,010 - HMPREF1058_RS05675 0.49 +0.0 106,056 + HMPREF1058_RS05675 0.54 +0.0 106,327 + HMPREF1058_RS05675 0.85 -0.8 106,327 + HMPREF1058_RS05675 0.85 -2.0
Or see this region's nucleotide sequence