Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS04050

Experiment: Rhamnogalacturonan from soy bean pectic fibre 5 mg/ml (C)

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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.

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500 ntHMPREF1058_RS04060 and HMPREF1058_RS04055 are separated by 9 nucleotidesHMPREF1058_RS04055 and HMPREF1058_RS04050 are separated by 39 nucleotidesHMPREF1058_RS04050 and HMPREF1058_RS04045 are separated by 19 nucleotidesHMPREF1058_RS04045 and HMPREF1058_RS04040 are separated by 10 nucleotides HMPREF1058_RS04060: HMPREF1058_RS04060 - VWA domain-containing protein, at 124,244 to 125,266 _RS04060 HMPREF1058_RS04055: HMPREF1058_RS04055 - tetratricopeptide repeat protein, at 125,276 to 125,983 _RS04055 HMPREF1058_RS04050: HMPREF1058_RS04050 - protein BatD, at 126,023 to 127,858 _RS04050 HMPREF1058_RS04045: HMPREF1058_RS04045 - tetratricopeptide repeat protein, at 127,878 to 128,696 _RS04045 HMPREF1058_RS04040: HMPREF1058_RS04040 - phosphatase PAP2 family protein, at 128,707 to 129,414 _RS04040 Position (kb) 126 127 128Strain fitness (log2 ratio) -3 -2 -1 0 1 2at 125.256 kb on + strandat 125.264 kb on + strandat 125.275 kb on + strandat 125.292 kb on - strandat 125.292 kb on - strandat 125.310 kb on + strandat 125.378 kb on + strand, within HMPREF1058_RS04055at 126.002 kb on + strandat 126.049 kb on - strandat 126.118 kb on - strandat 126.151 kb on + strandat 126.245 kb on - strand, within HMPREF1058_RS04050at 126.292 kb on + strand, within HMPREF1058_RS04050at 126.344 kb on - strand, within HMPREF1058_RS04050at 126.396 kb on + strand, within HMPREF1058_RS04050at 126.505 kb on + strand, within HMPREF1058_RS04050at 126.529 kb on + strand, within HMPREF1058_RS04050at 126.563 kb on + strand, within HMPREF1058_RS04050at 126.563 kb on + strand, within HMPREF1058_RS04050at 126.564 kb on - strand, within HMPREF1058_RS04050at 126.574 kb on + strand, within HMPREF1058_RS04050at 126.633 kb on + strand, within HMPREF1058_RS04050at 126.838 kb on + strand, within HMPREF1058_RS04050at 126.842 kb on + strand, within HMPREF1058_RS04050at 126.946 kb on + strand, within HMPREF1058_RS04050at 126.963 kb on + strand, within HMPREF1058_RS04050at 127.082 kb on + strand, within HMPREF1058_RS04050at 127.229 kb on - strand, within HMPREF1058_RS04050at 127.232 kb on + strand, within HMPREF1058_RS04050at 127.232 kb on + strand, within HMPREF1058_RS04050at 127.233 kb on - strand, within HMPREF1058_RS04050at 127.234 kb on + strand, within HMPREF1058_RS04050at 127.235 kb on - strand, within HMPREF1058_RS04050at 127.257 kb on - strand, within HMPREF1058_RS04050at 127.418 kb on + strand, within HMPREF1058_RS04050at 127.419 kb on - strand, within HMPREF1058_RS04050at 127.419 kb on - strand, within HMPREF1058_RS04050at 127.433 kb on - strand, within HMPREF1058_RS04050at 127.598 kb on + strand, within HMPREF1058_RS04050at 127.599 kb on - strand, within HMPREF1058_RS04050at 127.676 kb on - strandat 127.792 kb on + strandat 127.847 kb on - strandat 127.849 kb on - strandat 127.929 kb on + strandat 127.929 kb on + strandat 128.070 kb on + strand, within HMPREF1058_RS04045at 128.071 kb on - strand, within HMPREF1058_RS04045at 128.078 kb on + strand, within HMPREF1058_RS04045at 128.078 kb on + strand, within HMPREF1058_RS04045at 128.133 kb on + strand, within HMPREF1058_RS04045at 128.172 kb on + strand, within HMPREF1058_RS04045at 128.172 kb on + strand, within HMPREF1058_RS04045at 128.257 kb on + strand, within HMPREF1058_RS04045at 128.337 kb on - strand, within HMPREF1058_RS04045at 128.345 kb on + strand, within HMPREF1058_RS04045at 128.354 kb on + strand, within HMPREF1058_RS04045at 128.365 kb on + strand, within HMPREF1058_RS04045at 128.446 kb on + strand, within HMPREF1058_RS04045at 128.467 kb on + strand, within HMPREF1058_RS04045at 128.498 kb on + strand, within HMPREF1058_RS04045at 128.514 kb on - strand, within HMPREF1058_RS04045at 128.517 kb on - strand, within HMPREF1058_RS04045at 128.518 kb on + strand, within HMPREF1058_RS04045at 128.519 kb on - strand, within HMPREF1058_RS04045at 128.573 kb on - strand, within HMPREF1058_RS04045at 128.573 kb on - strand, within HMPREF1058_RS04045at 128.713 kb on - strandat 128.714 kb on + strandat 128.715 kb on - strandat 128.722 kb on + strandat 128.723 kb on - strandat 128.723 kb on - strandat 128.723 kb on - strandat 128.723 kb on - strandat 128.726 kb on + strandat 128.809 kb on - strand, within HMPREF1058_RS04040at 128.836 kb on - strand, within HMPREF1058_RS04040at 128.843 kb on + strand, within HMPREF1058_RS04040at 128.846 kb on - strandat 128.848 kb on - strand, within HMPREF1058_RS04040

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Per-strain Table

Position Strand Gene LocusTag Fraction Rhamnogalacturonan from soy bean pectic fibre 5 mg/ml (C)
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125,256 + +0.6
125,264 + -0.5
125,275 + +0.1
125,292 - -0.8
125,292 - -1.8
125,310 + -1.1
125,378 + HMPREF1058_RS04055 0.14 -0.8
126,002 + -0.7
126,049 - -0.8
126,118 - -1.8
126,151 + -1.3
126,245 - HMPREF1058_RS04050 0.12 -0.8
126,292 + HMPREF1058_RS04050 0.15 -1.8
126,344 - HMPREF1058_RS04050 0.17 -1.1
126,396 + HMPREF1058_RS04050 0.20 -2.9
126,505 + HMPREF1058_RS04050 0.26 -3.1
126,529 + HMPREF1058_RS04050 0.28 -1.8
126,563 + HMPREF1058_RS04050 0.29 -1.4
126,563 + HMPREF1058_RS04050 0.29 -1.8
126,564 - HMPREF1058_RS04050 0.29 -1.1
126,574 + HMPREF1058_RS04050 0.30 -1.7
126,633 + HMPREF1058_RS04050 0.33 -1.0
126,838 + HMPREF1058_RS04050 0.44 -1.7
126,842 + HMPREF1058_RS04050 0.45 -2.9
126,946 + HMPREF1058_RS04050 0.50 -1.3
126,963 + HMPREF1058_RS04050 0.51 -1.5
127,082 + HMPREF1058_RS04050 0.58 -2.8
127,229 - HMPREF1058_RS04050 0.66 -1.2
127,232 + HMPREF1058_RS04050 0.66 -0.3
127,232 + HMPREF1058_RS04050 0.66 -1.3
127,233 - HMPREF1058_RS04050 0.66 -0.5
127,234 + HMPREF1058_RS04050 0.66 -1.0
127,235 - HMPREF1058_RS04050 0.66 -0.1
127,257 - HMPREF1058_RS04050 0.67 -1.5
127,418 + HMPREF1058_RS04050 0.76 -0.8
127,419 - HMPREF1058_RS04050 0.76 -2.0
127,419 - HMPREF1058_RS04050 0.76 -0.3
127,433 - HMPREF1058_RS04050 0.77 -0.1
127,598 + HMPREF1058_RS04050 0.86 -1.8
127,599 - HMPREF1058_RS04050 0.86 -0.1
127,676 - -0.7
127,792 + -2.9
127,847 - -0.7
127,849 - -2.2
127,929 + +0.3
127,929 + -0.2
128,070 + HMPREF1058_RS04045 0.23 -2.5
128,071 - HMPREF1058_RS04045 0.24 -2.7
128,078 + HMPREF1058_RS04045 0.24 -2.4
128,078 + HMPREF1058_RS04045 0.24 -1.3
128,133 + HMPREF1058_RS04045 0.31 -0.5
128,172 + HMPREF1058_RS04045 0.36 -0.3
128,172 + HMPREF1058_RS04045 0.36 -0.5
128,257 + HMPREF1058_RS04045 0.46 -0.3
128,337 - HMPREF1058_RS04045 0.56 -0.3
128,345 + HMPREF1058_RS04045 0.57 -1.9
128,354 + HMPREF1058_RS04045 0.58 -2.9
128,365 + HMPREF1058_RS04045 0.59 -0.5
128,446 + HMPREF1058_RS04045 0.69 -1.7
128,467 + HMPREF1058_RS04045 0.72 -2.7
128,498 + HMPREF1058_RS04045 0.76 -2.0
128,514 - HMPREF1058_RS04045 0.78 -3.1
128,517 - HMPREF1058_RS04045 0.78 +0.2
128,518 + HMPREF1058_RS04045 0.78 -1.3
128,519 - HMPREF1058_RS04045 0.78 -2.8
128,573 - HMPREF1058_RS04045 0.85 -0.7
128,573 - HMPREF1058_RS04045 0.85 -2.4
128,713 - -1.1
128,714 + +0.7
128,715 - -1.3
128,722 + +0.5
128,723 - -0.5
128,723 - -1.9
128,723 - -0.5
128,723 - -0.8
128,726 + -1.3
128,809 - HMPREF1058_RS04040 0.14 -0.7
128,836 - HMPREF1058_RS04040 0.18 +0.2
128,843 + HMPREF1058_RS04040 0.19 -0.8
128,846 - +2.5
128,848 - HMPREF1058_RS04040 0.20 -0.7

Or see this region's nucleotide sequence