Strain Fitness in Phocaeicola vulgatus CL09T03C04 around HMPREF1058_RS19055

Experiment: Lacto-N-tetraose 10 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_RS19065 and HMPREF1058_RS19060 overlap by 4 nucleotidesHMPREF1058_RS19060 and HMPREF1058_RS0119250 are separated by 13 nucleotidesHMPREF1058_RS0119250 and HMPREF1058_RS19055 are separated by 75 nucleotidesHMPREF1058_RS19055 and HMPREF1058_RS19050 are separated by 6 nucleotidesHMPREF1058_RS19050 and HMPREF1058_RS20335 overlap by 11 nucleotidesHMPREF1058_RS20335 and HMPREF1058_RS19045 are separated by 5 nucleotidesHMPREF1058_RS19045 and HMPREF1058_RS20195 are separated by 7 nucleotides HMPREF1058_RS19065: HMPREF1058_RS19065 - helix-turn-helix domain-containing protein, at 27,714 to 28,025 _RS19065 HMPREF1058_RS19060: HMPREF1058_RS19060 - type II toxin-antitoxin system RelE/ParE family toxin, at 28,022 to 28,387 _RS19060 HMPREF1058_RS0119250: HMPREF1058_RS0119250 - hypothetical protein, at 28,401 to 28,688 _RS0119250 HMPREF1058_RS19055: HMPREF1058_RS19055 - hypothetical protein, at 28,764 to 29,039 _RS19055 HMPREF1058_RS19050: HMPREF1058_RS19050 - hypothetical protein, at 29,046 to 29,246 _RS19050 HMPREF1058_RS20335: HMPREF1058_RS20335 - DpnD/PcfM family protein, at 29,236 to 29,412 _RS20335 HMPREF1058_RS19045: HMPREF1058_RS19045 - hypothetical protein, at 29,418 to 29,828 _RS19045 HMPREF1058_RS20195: HMPREF1058_RS20195 - hypothetical protein, at 29,836 to 30,306 _RS20195 Position (kb) 28 29 30Strain fitness (log2 ratio) -3 -2 -1 0 1 2 3 4at 28.128 kb on - strand, within HMPREF1058_RS19060at 28.204 kb on - strand, within HMPREF1058_RS19060at 28.206 kb on - strand, within HMPREF1058_RS19060at 28.230 kb on - strand, within HMPREF1058_RS19060at 28.230 kb on - strand, within HMPREF1058_RS19060at 28.232 kb on - strand, within HMPREF1058_RS19060at 28.234 kb on - strand, within HMPREF1058_RS19060at 28.234 kb on - strand, within HMPREF1058_RS19060at 28.239 kb on - strand, within HMPREF1058_RS19060at 28.252 kb on - strand, within HMPREF1058_RS19060at 28.252 kb on - strand, within HMPREF1058_RS19060at 28.252 kb on - strand, within HMPREF1058_RS19060at 28.318 kb on - strand, within HMPREF1058_RS19060at 28.356 kb on - strandat 28.411 kb on - strandat 28.413 kb on - strandat 28.439 kb on + strand, within HMPREF1058_RS0119250at 28.439 kb on + strand, within HMPREF1058_RS0119250at 28.439 kb on + strand, within HMPREF1058_RS0119250at 28.440 kb on - strand, within HMPREF1058_RS0119250at 28.479 kb on + strand, within HMPREF1058_RS0119250at 28.532 kb on - strand, within HMPREF1058_RS0119250at 28.713 kb on - strandat 28.737 kb on + strandat 28.757 kb on + strandat 28.789 kb on + strandat 28.817 kb on - strand, within HMPREF1058_RS19055at 28.857 kb on - strand, within HMPREF1058_RS19055at 28.877 kb on - strand, within HMPREF1058_RS19055at 28.887 kb on - strand, within HMPREF1058_RS19055at 28.900 kb on + strand, within HMPREF1058_RS19055at 28.901 kb on - strand, within HMPREF1058_RS19055at 28.998 kb on + strand, within HMPREF1058_RS19055at 28.999 kb on - strand, within HMPREF1058_RS19055at 28.999 kb on - strandat 29.235 kb on - strandat 29.293 kb on - strand, within HMPREF1058_RS20335at 29.369 kb on - strand, within HMPREF1058_RS20335at 29.376 kb on + strand, within HMPREF1058_RS20335at 29.389 kb on + strand, within HMPREF1058_RS20335at 29.389 kb on + strand, within HMPREF1058_RS20335at 29.428 kb on - strandat 29.481 kb on - strand, within HMPREF1058_RS19045at 29.508 kb on - strand, within HMPREF1058_RS19045at 29.538 kb on + strand, within HMPREF1058_RS19045at 29.538 kb on + strand, within HMPREF1058_RS19045at 29.559 kb on - strand, within HMPREF1058_RS19045at 29.577 kb on + strand, within HMPREF1058_RS19045at 29.599 kb on + strand, within HMPREF1058_RS19045at 29.668 kb on - strand, within HMPREF1058_RS19045at 29.668 kb on - strand, within HMPREF1058_RS19045at 29.705 kb on - strand, within HMPREF1058_RS19045at 29.742 kb on + strand, within HMPREF1058_RS19045at 29.742 kb on + strand, within HMPREF1058_RS19045at 29.747 kb on - strand, within HMPREF1058_RS19045at 29.815 kb on - strandat 29.842 kb on + strandat 29.970 kb on + strand, within HMPREF1058_RS20195at 30.031 kb on - strand, within HMPREF1058_RS20195at 30.031 kb on - strand, within HMPREF1058_RS20195

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Per-strain Table

Position Strand Gene LocusTag Fraction Lacto-N-tetraose 10 mg/mL (C)
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28,128 - HMPREF1058_RS19060 0.29 +0.4
28,204 - HMPREF1058_RS19060 0.50 -0.5
28,206 - HMPREF1058_RS19060 0.50 -0.8
28,230 - HMPREF1058_RS19060 0.57 -0.2
28,230 - HMPREF1058_RS19060 0.57 +1.6
28,232 - HMPREF1058_RS19060 0.57 -0.4
28,234 - HMPREF1058_RS19060 0.58 -0.8
28,234 - HMPREF1058_RS19060 0.58 +1.1
28,239 - HMPREF1058_RS19060 0.59 +0.5
28,252 - HMPREF1058_RS19060 0.63 -0.3
28,252 - HMPREF1058_RS19060 0.63 +0.3
28,252 - HMPREF1058_RS19060 0.63 -0.6
28,318 - HMPREF1058_RS19060 0.81 -0.1
28,356 - +1.5
28,411 - +2.0
28,413 - +0.1
28,439 + HMPREF1058_RS0119250 0.13 +0.5
28,439 + HMPREF1058_RS0119250 0.13 +0.6
28,439 + HMPREF1058_RS0119250 0.13 -0.8
28,440 - HMPREF1058_RS0119250 0.14 +1.0
28,479 + HMPREF1058_RS0119250 0.27 +4.3
28,532 - HMPREF1058_RS0119250 0.45 +1.2
28,713 - -0.1
28,737 + +0.1
28,757 + +2.3
28,789 + -0.4
28,817 - HMPREF1058_RS19055 0.19 +0.6
28,857 - HMPREF1058_RS19055 0.34 -1.4
28,877 - HMPREF1058_RS19055 0.41 -3.0
28,887 - HMPREF1058_RS19055 0.45 -1.3
28,900 + HMPREF1058_RS19055 0.49 -0.4
28,901 - HMPREF1058_RS19055 0.50 +0.5
28,998 + HMPREF1058_RS19055 0.85 +0.1
28,999 - HMPREF1058_RS19055 0.85 +0.1
28,999 - +1.1
29,235 - +0.1
29,293 - HMPREF1058_RS20335 0.32 +0.6
29,369 - HMPREF1058_RS20335 0.75 -1.3
29,376 + HMPREF1058_RS20335 0.79 +0.7
29,389 + HMPREF1058_RS20335 0.86 -1.7
29,389 + HMPREF1058_RS20335 0.86 -1.6
29,428 - -0.4
29,481 - HMPREF1058_RS19045 0.15 -2.6
29,508 - HMPREF1058_RS19045 0.22 -0.9
29,538 + HMPREF1058_RS19045 0.29 -2.6
29,538 + HMPREF1058_RS19045 0.29 +0.5
29,559 - HMPREF1058_RS19045 0.34 -0.3
29,577 + HMPREF1058_RS19045 0.39 -2.4
29,599 + HMPREF1058_RS19045 0.44 -0.2
29,668 - HMPREF1058_RS19045 0.61 +0.3
29,668 - HMPREF1058_RS19045 0.61 +0.6
29,705 - HMPREF1058_RS19045 0.70 +1.5
29,742 + HMPREF1058_RS19045 0.79 +0.0
29,742 + HMPREF1058_RS19045 0.79 +1.5
29,747 - HMPREF1058_RS19045 0.80 -1.7
29,815 - -0.2
29,842 + +0.2
29,970 + HMPREF1058_RS20195 0.28 -0.7
30,031 - HMPREF1058_RS20195 0.41 +0.4
30,031 - HMPREF1058_RS20195 0.41 -0.4

Or see this region's nucleotide sequence