Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS12110

Experiment: Rhamnogalacturonan from soy bean pectic fibre 2.5 mg/ml (C)

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_RS12120 and HMPREF1058_RS12115 are separated by 63 nucleotidesHMPREF1058_RS12115 and HMPREF1058_RS12110 are separated by 4 nucleotidesHMPREF1058_RS12110 and HMPREF1058_RS12105 are separated by 41 nucleotidesHMPREF1058_RS12105 and HMPREF1058_RS12100 overlap by 4 nucleotides HMPREF1058_RS12120: HMPREF1058_RS12120 - RNA polymerase sigma factor, at 196,507 to 197,016 _RS12120 HMPREF1058_RS12115: HMPREF1058_RS12115 - acetylglutamate kinase, at 197,080 to 197,853 _RS12115 HMPREF1058_RS12110: HMPREF1058_RS12110 - biosynthetic arginine decarboxylase, at 197,858 to 199,750 _RS12110 HMPREF1058_RS12105: HMPREF1058_RS12105 - shikimate kinase, at 199,792 to 200,319 _RS12105 HMPREF1058_RS12100: HMPREF1058_RS12100 - type I DNA topoisomerase, at 200,316 to 202,754 _RS12100 Position (kb) 197 198 199 200Strain fitness (log2 ratio) -4 -3 -2 -1 0 1 2at 196.947 kb on + strand, within HMPREF1058_RS12120at 196.964 kb on + strand, within HMPREF1058_RS12120at 196.965 kb on - strand, within HMPREF1058_RS12120at 197.024 kb on + strandat 197.135 kb on - strandat 197.135 kb on - strandat 197.245 kb on - strand, within HMPREF1058_RS12115at 197.287 kb on + strand, within HMPREF1058_RS12115at 197.288 kb on - strand, within HMPREF1058_RS12115at 197.310 kb on - strand, within HMPREF1058_RS12115at 197.368 kb on - strand, within HMPREF1058_RS12115at 197.471 kb on - strand, within HMPREF1058_RS12115at 197.625 kb on - strand, within HMPREF1058_RS12115at 197.626 kb on + strand, within HMPREF1058_RS12115at 197.626 kb on + strand, within HMPREF1058_RS12115at 197.626 kb on + strand, within HMPREF1058_RS12115at 197.627 kb on - strand, within HMPREF1058_RS12115at 197.627 kb on - strandat 197.699 kb on - strand, within HMPREF1058_RS12115at 197.751 kb on + strand, within HMPREF1058_RS12115at 197.751 kb on + strand, within HMPREF1058_RS12115at 197.761 kb on + strand, within HMPREF1058_RS12115at 197.761 kb on + strand, within HMPREF1058_RS12115at 197.761 kb on + strand, within HMPREF1058_RS12115at 197.790 kb on + strandat 197.830 kb on + strandat 197.831 kb on - strandat 197.835 kb on + strandat 197.857 kb on - strandat 197.868 kb on + strandat 197.872 kb on + strandat 197.872 kb on + strandat 197.873 kb on - strandat 197.880 kb on + strandat 197.881 kb on - strandat 197.896 kb on - strandat 197.899 kb on + strandat 197.899 kb on + strandat 197.975 kb on - strandat 197.997 kb on + strandat 197.997 kb on + strandat 197.998 kb on - strandat 198.006 kb on + strandat 198.007 kb on - strandat 198.041 kb on + strandat 198.095 kb on - strand, within HMPREF1058_RS12110at 198.152 kb on + strand, within HMPREF1058_RS12110at 198.153 kb on - strand, within HMPREF1058_RS12110at 198.153 kb on - strand, within HMPREF1058_RS12110at 198.159 kb on - strand, within HMPREF1058_RS12110at 198.161 kb on - strand, within HMPREF1058_RS12110at 198.163 kb on - strand, within HMPREF1058_RS12110at 198.209 kb on + strand, within HMPREF1058_RS12110at 198.210 kb on - strand, within HMPREF1058_RS12110at 198.210 kb on - strand, within HMPREF1058_RS12110at 198.226 kb on + strand, within HMPREF1058_RS12110at 198.274 kb on + strand, within HMPREF1058_RS12110at 198.326 kb on + strand, within HMPREF1058_RS12110at 198.480 kb on + strand, within HMPREF1058_RS12110at 198.492 kb on - strandat 198.534 kb on - strand, within HMPREF1058_RS12110at 198.757 kb on + strand, within HMPREF1058_RS12110at 198.809 kb on - strand, within HMPREF1058_RS12110at 198.822 kb on + strand, within HMPREF1058_RS12110at 198.837 kb on + strand, within HMPREF1058_RS12110at 198.838 kb on - strand, within HMPREF1058_RS12110at 199.010 kb on + strandat 199.011 kb on - strand, within HMPREF1058_RS12110at 199.012 kb on + strand, within HMPREF1058_RS12110at 199.168 kb on + strand, within HMPREF1058_RS12110at 199.173 kb on - strand, within HMPREF1058_RS12110at 199.178 kb on - strand, within HMPREF1058_RS12110at 199.178 kb on - strand, within HMPREF1058_RS12110at 199.308 kb on + strand, within HMPREF1058_RS12110at 199.487 kb on - strand, within HMPREF1058_RS12110at 199.488 kb on + strand, within HMPREF1058_RS12110at 199.513 kb on + strand, within HMPREF1058_RS12110at 199.537 kb on + strand, within HMPREF1058_RS12110at 199.573 kb on + strandat 199.574 kb on - strandat 199.574 kb on - strandat 199.659 kb on - strandat 199.713 kb on + strandat 199.713 kb on + strandat 199.775 kb on + strandat 199.776 kb on - strandat 199.785 kb on + strandat 199.785 kb on + strandat 199.786 kb on - strandat 199.787 kb on + strandat 199.789 kb on + strandat 199.790 kb on - strandat 199.793 kb on + strandat 199.797 kb on + strandat 199.846 kb on - strand, within HMPREF1058_RS12105at 200.049 kb on + strand, within HMPREF1058_RS12105at 200.050 kb on - strand, within HMPREF1058_RS12105at 200.051 kb on + strand, within HMPREF1058_RS12105at 200.051 kb on + strand, within HMPREF1058_RS12105at 200.052 kb on - strand, within HMPREF1058_RS12105at 200.196 kb on + strand, within HMPREF1058_RS12105at 200.269 kb on + strandat 200.294 kb on + strandat 200.294 kb on + strandat 200.295 kb on - strandat 200.299 kb on + strandat 200.302 kb on + strandat 200.310 kb on + strandat 200.310 kb on + strandat 200.310 kb on + strandat 200.343 kb on + strandat 200.442 kb on - strandat 200.558 kb on - strandat 200.643 kb on - strand, within HMPREF1058_RS12100at 200.735 kb on - strand, within HMPREF1058_RS12100

download strain data

Per-strain Table

Position Strand Gene LocusTag Fraction Rhamnogalacturonan from soy bean pectic fibre 2.5 mg/ml (C)
remove
196,947 + HMPREF1058_RS12120 0.86 -1.3
196,964 + HMPREF1058_RS12120 0.90 -0.1
196,965 - HMPREF1058_RS12120 0.90 +1.3
197,024 + -1.9
197,135 - -3.1
197,135 - +0.0
197,245 - HMPREF1058_RS12115 0.21 -1.7
197,287 + HMPREF1058_RS12115 0.27 -0.4
197,288 - HMPREF1058_RS12115 0.27 +1.4
197,310 - HMPREF1058_RS12115 0.30 -1.8
197,368 - HMPREF1058_RS12115 0.37 -4.0
197,471 - HMPREF1058_RS12115 0.51 -3.3
197,625 - HMPREF1058_RS12115 0.70 -3.6
197,626 + HMPREF1058_RS12115 0.71 -2.4
197,626 + HMPREF1058_RS12115 0.71 -2.0
197,626 + HMPREF1058_RS12115 0.71 -2.7
197,627 - HMPREF1058_RS12115 0.71 -2.6
197,627 - +0.1
197,699 - HMPREF1058_RS12115 0.80 -3.7
197,751 + HMPREF1058_RS12115 0.87 -0.3
197,751 + HMPREF1058_RS12115 0.87 -0.7
197,761 + HMPREF1058_RS12115 0.88 -3.5
197,761 + HMPREF1058_RS12115 0.88 -3.2
197,761 + HMPREF1058_RS12115 0.88 -1.9
197,790 + -1.0
197,830 + -3.4
197,831 - -3.4
197,835 + -2.5
197,857 - -1.8
197,868 + -1.8
197,872 + -3.4
197,872 + -3.8
197,873 - -0.3
197,880 + -2.1
197,881 - -0.1
197,896 - -1.3
197,899 + -3.5
197,899 + -2.1
197,975 - -1.5
197,997 + -2.6
197,997 + -3.7
197,998 - -0.3
198,006 + -2.5
198,007 - -1.6
198,041 + -1.3
198,095 - HMPREF1058_RS12110 0.13 -0.4
198,152 + HMPREF1058_RS12110 0.16 -3.7
198,153 - HMPREF1058_RS12110 0.16 -1.3
198,153 - HMPREF1058_RS12110 0.16 -1.7
198,159 - HMPREF1058_RS12110 0.16 -0.7
198,161 - HMPREF1058_RS12110 0.16 -0.3
198,163 - HMPREF1058_RS12110 0.16 +0.2
198,209 + HMPREF1058_RS12110 0.19 -1.8
198,210 - HMPREF1058_RS12110 0.19 -0.4
198,210 - HMPREF1058_RS12110 0.19 -0.8
198,226 + HMPREF1058_RS12110 0.19 -1.9
198,274 + HMPREF1058_RS12110 0.22 -2.1
198,326 + HMPREF1058_RS12110 0.25 -1.6
198,480 + HMPREF1058_RS12110 0.33 -3.3
198,492 - -0.0
198,534 - HMPREF1058_RS12110 0.36 -1.8
198,757 + HMPREF1058_RS12110 0.47 -2.1
198,809 - HMPREF1058_RS12110 0.50 -0.2
198,822 + HMPREF1058_RS12110 0.51 -4.0
198,837 + HMPREF1058_RS12110 0.52 -2.1
198,838 - HMPREF1058_RS12110 0.52 -0.4
199,010 + +2.4
199,011 - HMPREF1058_RS12110 0.61 -0.8
199,012 + HMPREF1058_RS12110 0.61 -2.4
199,168 + HMPREF1058_RS12110 0.69 -3.1
199,173 - HMPREF1058_RS12110 0.69 -0.4
199,178 - HMPREF1058_RS12110 0.70 -3.0
199,178 - HMPREF1058_RS12110 0.70 -0.1
199,308 + HMPREF1058_RS12110 0.77 -1.1
199,487 - HMPREF1058_RS12110 0.86 -1.8
199,488 + HMPREF1058_RS12110 0.86 -1.1
199,513 + HMPREF1058_RS12110 0.87 -3.2
199,537 + HMPREF1058_RS12110 0.89 -3.3
199,573 + -3.2
199,574 - -1.9
199,574 - -0.0
199,659 - -0.8
199,713 + -2.6
199,713 + -4.1
199,775 + -0.2
199,776 - +0.5
199,785 + -2.8
199,785 + -4.2
199,786 - +0.4
199,787 + -2.5
199,789 + -3.7
199,790 - -0.2
199,793 + -3.7
199,797 + -1.6
199,846 - HMPREF1058_RS12105 0.10 -1.1
200,049 + HMPREF1058_RS12105 0.49 -2.9
200,050 - HMPREF1058_RS12105 0.49 -3.3
200,051 + HMPREF1058_RS12105 0.49 -1.1
200,051 + HMPREF1058_RS12105 0.49 -2.3
200,052 - HMPREF1058_RS12105 0.49 -0.5
200,196 + HMPREF1058_RS12105 0.77 -2.5
200,269 + -1.5
200,294 + -2.7
200,294 + -0.1
200,295 - -2.8
200,299 + -2.9
200,302 + +1.4
200,310 + -3.1
200,310 + -3.2
200,310 + -3.0
200,343 + +0.4
200,442 - -0.4
200,558 - +1.0
200,643 - HMPREF1058_RS12100 0.13 -0.4
200,735 - HMPREF1058_RS12100 0.17 -0.9

Or see this region's nucleotide sequence