Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS04085

Experiment: diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse17; day5

Add experiment(s):

Zoom: Pan:

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.

download SVG
500 ntHMPREF1058_RS04095 and HMPREF1058_RS04090 are separated by 73 nucleotidesHMPREF1058_RS04090 and HMPREF1058_RS04085 are separated by 25 nucleotidesHMPREF1058_RS04085 and HMPREF1058_RS04080 are separated by 283 nucleotides HMPREF1058_RS04095: HMPREF1058_RS04095 - 30S ribosomal protein S12 methylthiotransferase RimO, at 116,612 to 117,910 _RS04095 HMPREF1058_RS04090: HMPREF1058_RS04090 - HU family DNA-binding protein, at 117,984 to 118,256 _RS04090 HMPREF1058_RS04085: HMPREF1058_RS04085 - HU family DNA-binding protein, at 118,282 to 119,712 _RS04085 HMPREF1058_RS04080: HMPREF1058_RS04080 - AAA family ATPase, at 119,996 to 120,991 _RS04080 Position (kb) 118 119 120Strain fitness (log2 ratio) -5 -4 -3 -2 -1 0 1 2 3 4at 117.345 kb on + strand, within HMPREF1058_RS04095at 117.346 kb on - strand, within HMPREF1058_RS04095at 117.353 kb on + strand, within HMPREF1058_RS04095at 117.389 kb on - strand, within HMPREF1058_RS04095at 117.414 kb on + strand, within HMPREF1058_RS04095at 117.414 kb on + strand, within HMPREF1058_RS04095at 117.477 kb on + strand, within HMPREF1058_RS04095at 117.477 kb on + strand, within HMPREF1058_RS04095at 117.482 kb on - strand, within HMPREF1058_RS04095at 117.613 kb on + strand, within HMPREF1058_RS04095at 117.761 kb on + strand, within HMPREF1058_RS04095at 117.761 kb on + strand, within HMPREF1058_RS04095at 117.762 kb on - strand, within HMPREF1058_RS04095at 117.765 kb on - strand, within HMPREF1058_RS04095at 117.833 kb on + strandat 117.892 kb on - strandat 117.958 kb on + strandat 118.031 kb on + strand, within HMPREF1058_RS04090at 118.031 kb on + strand, within HMPREF1058_RS04090at 118.032 kb on - strand, within HMPREF1058_RS04090at 118.032 kb on - strand, within HMPREF1058_RS04090at 118.044 kb on - strand, within HMPREF1058_RS04090at 118.254 kb on + strandat 118.254 kb on + strandat 118.255 kb on - strandat 118.266 kb on + strandat 118.266 kb on + strandat 118.266 kb on + strandat 118.278 kb on + strandat 118.296 kb on - strandat 118.301 kb on + strandat 118.302 kb on - strandat 118.302 kb on - strandat 118.308 kb on + strandat 118.400 kb on + strandat 118.418 kb on + strandat 118.418 kb on + strandat 118.438 kb on - strand, within HMPREF1058_RS04085at 118.564 kb on - strand, within HMPREF1058_RS04085at 118.592 kb on + strand, within HMPREF1058_RS04085at 118.595 kb on + strand, within HMPREF1058_RS04085at 118.635 kb on - strand, within HMPREF1058_RS04085at 118.728 kb on + strand, within HMPREF1058_RS04085at 118.849 kb on - strand, within HMPREF1058_RS04085at 118.851 kb on - strand, within HMPREF1058_RS04085at 119.100 kb on - strand, within HMPREF1058_RS04085at 119.102 kb on + strand, within HMPREF1058_RS04085at 119.102 kb on + strand, within HMPREF1058_RS04085at 119.102 kb on + strand, within HMPREF1058_RS04085at 119.205 kb on + strand, within HMPREF1058_RS04085at 119.246 kb on + strand, within HMPREF1058_RS04085at 119.249 kb on - strand, within HMPREF1058_RS04085at 119.249 kb on - strand, within HMPREF1058_RS04085at 119.370 kb on + strand, within HMPREF1058_RS04085at 119.371 kb on - strand, within HMPREF1058_RS04085at 119.438 kb on + strand, within HMPREF1058_RS04085at 119.439 kb on - strand, within HMPREF1058_RS04085at 119.513 kb on + strand, within HMPREF1058_RS04085at 119.513 kb on + strand, within HMPREF1058_RS04085at 119.514 kb on - strand, within HMPREF1058_RS04085at 119.525 kb on + strand, within HMPREF1058_RS04085at 119.541 kb on + strand, within HMPREF1058_RS04085at 119.545 kb on + strand, within HMPREF1058_RS04085at 119.594 kb on - strandat 119.646 kb on + strandat 119.646 kb on + strandat 119.647 kb on - strandat 119.746 kb on + strandat 119.858 kb on - strandat 119.981 kb on + strandat 120.093 kb on + strandat 120.120 kb on + strand, within HMPREF1058_RS04080at 120.121 kb on - strand, within HMPREF1058_RS04080at 120.132 kb on + strand, within HMPREF1058_RS04080at 120.224 kb on + strand, within HMPREF1058_RS04080at 120.359 kb on - strand, within HMPREF1058_RS04080at 120.440 kb on - strand, within HMPREF1058_RS04080at 120.462 kb on + strand, within HMPREF1058_RS04080at 120.678 kb on - strand, within HMPREF1058_RS04080at 120.694 kb on - strand, within HMPREF1058_RS04080at 120.701 kb on + strand, within HMPREF1058_RS04080at 120.702 kb on - strand, within HMPREF1058_RS04080

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse17; day5
remove
117,345 + HMPREF1058_RS04095 0.56 +1.6
117,346 - HMPREF1058_RS04095 0.57 -0.3
117,353 + HMPREF1058_RS04095 0.57 +1.3
117,389 - HMPREF1058_RS04095 0.60 +0.2
117,414 + HMPREF1058_RS04095 0.62 -0.2
117,414 + HMPREF1058_RS04095 0.62 -0.2
117,477 + HMPREF1058_RS04095 0.67 +1.7
117,477 + HMPREF1058_RS04095 0.67 +1.5
117,482 - HMPREF1058_RS04095 0.67 -0.4
117,613 + HMPREF1058_RS04095 0.77 +4.1
117,761 + HMPREF1058_RS04095 0.88 +1.0
117,761 + HMPREF1058_RS04095 0.88 +0.0
117,762 - HMPREF1058_RS04095 0.89 -1.6
117,765 - HMPREF1058_RS04095 0.89 -0.1
117,833 + +0.4
117,892 - -0.1
117,958 + +0.6
118,031 + HMPREF1058_RS04090 0.17 -0.1
118,031 + HMPREF1058_RS04090 0.17 -3.0
118,032 - HMPREF1058_RS04090 0.18 -1.8
118,032 - HMPREF1058_RS04090 0.18 +0.3
118,044 - HMPREF1058_RS04090 0.22 -1.8
118,254 + +0.9
118,254 + -1.5
118,255 - -0.8
118,266 + +0.0
118,266 + -0.7
118,266 + +0.2
118,278 + -0.1
118,296 - +0.7
118,301 + -0.6
118,302 - +1.0
118,302 - -1.1
118,308 + -1.7
118,400 + -1.2
118,418 + -0.3
118,418 + -0.8
118,438 - HMPREF1058_RS04085 0.11 -3.6
118,564 - HMPREF1058_RS04085 0.20 -1.7
118,592 + HMPREF1058_RS04085 0.22 -0.1
118,595 + HMPREF1058_RS04085 0.22 -1.9
118,635 - HMPREF1058_RS04085 0.25 -0.7
118,728 + HMPREF1058_RS04085 0.31 -1.2
118,849 - HMPREF1058_RS04085 0.40 -2.3
118,851 - HMPREF1058_RS04085 0.40 -1.0
119,100 - HMPREF1058_RS04085 0.57 +0.0
119,102 + HMPREF1058_RS04085 0.57 -0.8
119,102 + HMPREF1058_RS04085 0.57 -0.6
119,102 + HMPREF1058_RS04085 0.57 -1.0
119,205 + HMPREF1058_RS04085 0.65 -1.9
119,246 + HMPREF1058_RS04085 0.67 -1.0
119,249 - HMPREF1058_RS04085 0.68 -0.7
119,249 - HMPREF1058_RS04085 0.68 -1.4
119,370 + HMPREF1058_RS04085 0.76 -1.6
119,371 - HMPREF1058_RS04085 0.76 -1.2
119,438 + HMPREF1058_RS04085 0.81 -0.6
119,439 - HMPREF1058_RS04085 0.81 +0.9
119,513 + HMPREF1058_RS04085 0.86 +0.0
119,513 + HMPREF1058_RS04085 0.86 -1.2
119,514 - HMPREF1058_RS04085 0.86 -0.4
119,525 + HMPREF1058_RS04085 0.87 +0.3
119,541 + HMPREF1058_RS04085 0.88 -0.7
119,545 + HMPREF1058_RS04085 0.88 +0.4
119,594 - -1.1
119,646 + +0.9
119,646 + +0.1
119,647 - +0.2
119,746 + +0.0
119,858 - -1.6
119,981 + -1.3
120,093 + -2.6
120,120 + HMPREF1058_RS04080 0.12 -2.9
120,121 - HMPREF1058_RS04080 0.13 -2.6
120,132 + HMPREF1058_RS04080 0.14 -2.8
120,224 + HMPREF1058_RS04080 0.23 -2.2
120,359 - HMPREF1058_RS04080 0.36 -2.6
120,440 - HMPREF1058_RS04080 0.45 -5.5
120,462 + HMPREF1058_RS04080 0.47 -3.3
120,678 - HMPREF1058_RS04080 0.68 -1.6
120,694 - HMPREF1058_RS04080 0.70 -3.2
120,701 + HMPREF1058_RS04080 0.71 -2.2
120,702 - HMPREF1058_RS04080 0.71 -3.8

Or see this region's nucleotide sequence