Experiment: PDB
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 DDA3937_RS01715 and DDA3937_RS01720 are separated by 685 nucleotides DDA3937_RS01720 and DDA3937_RS01725 are separated by 178 nucleotides
DDA3937_RS01715: DDA3937_RS01715 - 16S rRNA (cytidine(1402)-2'-O)-methyltransferase, at 379,805 to 380,674
_RS01715
DDA3937_RS01720: DDA3937_RS01720 - shikimate 5-dehydrogenase, at 381,360 to 382,169
_RS01720
DDA3937_RS01725: DDA3937_RS01725 - 4,5-DOPA dioxygenase extradiol, at 382,348 to 383,136
_RS01725
Position (kb) 381
382
383 Strain fitness (log2 ratio) -4
-3
-2
-1
0
1
2
3 at 380.375 kb on + strand, within DDA3937_RS01715 at 380.375 kb on + strand, within DDA3937_RS01715 at 380.375 kb on + strand, within DDA3937_RS01715 at 380.421 kb on - strand at 380.421 kb on - strand, within DDA3937_RS01715 at 380.636 kb on + strand at 380.672 kb on + strand at 381.111 kb on + strand at 381.112 kb on - strand at 381.201 kb on - strand at 381.284 kb on + strand at 381.284 kb on + strand at 381.285 kb on - strand at 381.298 kb on + strand at 381.299 kb on - strand at 381.299 kb on - strand at 381.299 kb on - strand at 381.299 kb on - strand at 381.299 kb on - strand at 381.328 kb on + strand at 381.328 kb on + strand at 381.328 kb on + strand at 381.328 kb on + strand at 381.329 kb on - strand at 381.329 kb on - strand at 381.329 kb on - strand at 381.329 kb on - strand at 381.329 kb on - strand at 381.329 kb on - strand at 381.360 kb on - strand at 381.411 kb on - strand at 381.411 kb on - strand at 381.411 kb on - strand at 381.413 kb on + strand at 381.413 kb on + strand at 381.413 kb on + strand at 381.414 kb on - strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.415 kb on + strand at 381.416 kb on - strand at 381.416 kb on - strand at 381.416 kb on - strand at 381.416 kb on - strand at 381.416 kb on - strand at 381.416 kb on - strand at 381.420 kb on - strand at 381.420 kb on - strand at 381.420 kb on - strand at 381.435 kb on + strand at 381.435 kb on + strand at 381.436 kb on - strand at 381.465 kb on - strand at 381.465 kb on - strand, within DDA3937_RS01720 at 381.466 kb on + strand, within DDA3937_RS01720 at 381.467 kb on - strand, within DDA3937_RS01720 at 381.467 kb on - strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.468 kb on + strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.469 kb on - strand, within DDA3937_RS01720 at 381.470 kb on + strand, within DDA3937_RS01720 at 381.470 kb on + strand, within DDA3937_RS01720 at 381.471 kb on - strand, within DDA3937_RS01720 at 381.471 kb on - strand, within DDA3937_RS01720 at 381.471 kb on - strand, within DDA3937_RS01720 at 381.479 kb on + strand, within DDA3937_RS01720 at 381.483 kb on - strand, within DDA3937_RS01720 at 381.491 kb on + strand at 381.492 kb on - strand, within DDA3937_RS01720 at 381.506 kb on - strand, within DDA3937_RS01720 at 381.569 kb on + strand, within DDA3937_RS01720 at 381.584 kb on + strand, within DDA3937_RS01720 at 381.584 kb on + strand, within DDA3937_RS01720 at 381.621 kb on - strand at 381.623 kb on + strand, within DDA3937_RS01720 at 381.623 kb on + strand, within DDA3937_RS01720 at 381.623 kb on + strand, within DDA3937_RS01720 at 381.623 kb on + strand, within DDA3937_RS01720 at 381.624 kb on - strand, within DDA3937_RS01720 at 381.624 kb on - strand, within DDA3937_RS01720 at 381.624 kb on - strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.626 kb on + strand, within DDA3937_RS01720 at 381.627 kb on - strand, within DDA3937_RS01720 at 381.657 kb on + strand, within DDA3937_RS01720 at 381.658 kb on - strand, within DDA3937_RS01720 at 381.658 kb on - strand, within DDA3937_RS01720 at 381.662 kb on + strand, within DDA3937_RS01720 at 381.669 kb on + strand, within DDA3937_RS01720 at 381.669 kb on + strand, within DDA3937_RS01720 at 381.671 kb on + strand, within DDA3937_RS01720 at 381.672 kb on - strand, within DDA3937_RS01720 at 381.672 kb on - strand, within DDA3937_RS01720 at 381.681 kb on - strand, within DDA3937_RS01720 at 381.730 kb on + strand, within DDA3937_RS01720 at 381.730 kb on + strand, within DDA3937_RS01720 at 381.730 kb on + strand, within DDA3937_RS01720 at 381.801 kb on - strand, within DDA3937_RS01720 at 381.846 kb on + strand, within DDA3937_RS01720 at 381.847 kb on - strand, within DDA3937_RS01720 at 381.847 kb on - strand, within DDA3937_RS01720 at 381.847 kb on - strand, within DDA3937_RS01720 at 381.878 kb on + strand, within DDA3937_RS01720 at 381.879 kb on - strand, within DDA3937_RS01720 at 381.879 kb on - strand, within DDA3937_RS01720 at 381.880 kb on + strand, within DDA3937_RS01720 at 381.880 kb on + strand, within DDA3937_RS01720 at 381.880 kb on + strand, within DDA3937_RS01720 at 381.880 kb on + strand, within DDA3937_RS01720 at 381.967 kb on + strand, within DDA3937_RS01720 at 381.967 kb on + strand, within DDA3937_RS01720 at 381.967 kb on + strand, within DDA3937_RS01720 at 381.983 kb on + strand, within DDA3937_RS01720 at 381.984 kb on - strand, within DDA3937_RS01720 at 382.021 kb on + strand, within DDA3937_RS01720 at 382.021 kb on + strand, within DDA3937_RS01720 at 382.022 kb on - strand, within DDA3937_RS01720 at 382.107 kb on + strand at 382.155 kb on + strand at 382.156 kb on - strand at 382.183 kb on + strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.184 kb on - strand at 382.186 kb on + strand at 382.186 kb on + strand at 382.186 kb on + strand at 382.186 kb on + strand at 382.186 kb on + strand at 382.186 kb on + strand at 382.213 kb on + strand at 382.219 kb on + strand at 382.219 kb on + strand at 382.219 kb on + strand at 382.219 kb on + strand at 382.219 kb on + strand at 382.220 kb on - strand at 382.220 kb on - strand at 382.275 kb on + strand at 382.275 kb on + strand at 382.275 kb on + strand at 382.276 kb on - strand at 382.276 kb on - strand at 382.290 kb on - strand at 382.295 kb on + strand at 382.295 kb on + strand at 382.296 kb on - strand at 382.296 kb on - strand at 382.300 kb on + strand at 382.300 kb on + strand at 382.300 kb on + strand at 382.301 kb on - strand at 382.314 kb on - strand at 382.321 kb on - strand at 382.342 kb on - strand at 382.342 kb on - strand at 382.342 kb on - strand at 382.347 kb on + strand at 382.420 kb on + strand at 382.437 kb on + strand, within DDA3937_RS01725 at 382.475 kb on + strand, within DDA3937_RS01725 at 382.476 kb on - strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.495 kb on + strand, within DDA3937_RS01725 at 382.496 kb on - strand, within DDA3937_RS01725 at 382.496 kb on - strand, within DDA3937_RS01725 at 382.496 kb on - strand, within DDA3937_RS01725 at 382.496 kb on - strand, within DDA3937_RS01725 at 382.528 kb on - strand, within DDA3937_RS01725 at 382.528 kb on - strand, within DDA3937_RS01725 at 382.651 kb on + strand, within DDA3937_RS01725 at 382.651 kb on + strand, within DDA3937_RS01725 at 382.652 kb on - strand, within DDA3937_RS01725 at 382.652 kb on - strand, within DDA3937_RS01725 at 382.652 kb on - strand, within DDA3937_RS01725 at 382.652 kb on - strand, within DDA3937_RS01725 at 382.725 kb on + strand, within DDA3937_RS01725 at 382.771 kb on + strand, within DDA3937_RS01725 at 382.777 kb on + strand, within DDA3937_RS01725 at 382.777 kb on + strand, within DDA3937_RS01725 at 382.791 kb on + strand, within DDA3937_RS01725 at 382.792 kb on - strand, within DDA3937_RS01725 at 382.792 kb on - strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.038 kb on + strand, within DDA3937_RS01725 at 383.039 kb on - strand, within DDA3937_RS01725 at 383.039 kb on - strand, within DDA3937_RS01725 at 383.039 kb on - strand, within DDA3937_RS01725 at 383.039 kb on - strand, within DDA3937_RS01725 at 383.039 kb on - strand, within DDA3937_RS01725 at 383.151 kb on - strand at 383.166 kb on + strand at 383.166 kb on + strand at 383.167 kb on - strand
Per-strain Table
Position Strand Gene LocusTag Fraction PDB remove 380,375 + DDA3937_RS01715 0.66 -0.2 380,375 + DDA3937_RS01715 0.66 -1.0 380,375 + DDA3937_RS01715 0.66 -0.8 380,421 - +0.0 380,421 - DDA3937_RS01715 0.71 +0.1 380,636 + +0.0 380,672 + -1.0 381,111 + +0.7 381,112 - +1.5 381,201 - +0.8 381,284 + -1.8 381,284 + +1.4 381,285 - -3.0 381,298 + -0.6 381,299 - +1.6 381,299 - -2.2 381,299 - -3.7 381,299 - +0.7 381,299 - +0.9 381,328 + -1.0 381,328 + -0.4 381,328 + +1.1 381,328 + +1.4 381,329 - -1.0 381,329 - +0.7 381,329 - +1.0 381,329 - -0.6 381,329 - -0.6 381,329 - -1.4 381,360 - +1.3 381,411 - -2.7 381,411 - +0.8 381,411 - -0.6 381,413 + +0.1 381,413 + +0.1 381,413 + -1.6 381,414 - -0.1 381,415 + -1.8 381,415 + -0.7 381,415 + +0.2 381,415 + -0.1 381,415 + -0.9 381,415 + -3.1 381,415 + +0.5 381,416 - +0.0 381,416 - -2.0 381,416 - -1.6 381,416 - +0.9 381,416 - -1.7 381,416 - +1.9 381,420 - -1.6 381,420 - +1.2 381,420 - +1.6 381,435 + +2.0 381,435 + +0.1 381,436 - +0.6 381,465 - +0.0 381,465 - DDA3937_RS01720 0.13 -1.0 381,466 + DDA3937_RS01720 0.13 +1.0 381,467 - DDA3937_RS01720 0.13 +0.2 381,467 - DDA3937_RS01720 0.13 -0.1 381,468 + DDA3937_RS01720 0.13 +1.1 381,468 + DDA3937_RS01720 0.13 -0.4 381,468 + DDA3937_RS01720 0.13 -0.8 381,468 + DDA3937_RS01720 0.13 -1.4 381,468 + DDA3937_RS01720 0.13 -1.6 381,468 + DDA3937_RS01720 0.13 -0.4 381,468 + DDA3937_RS01720 0.13 -2.2 381,468 + DDA3937_RS01720 0.13 -0.6 381,468 + DDA3937_RS01720 0.13 -1.8 381,469 - DDA3937_RS01720 0.13 +3.4 381,469 - DDA3937_RS01720 0.13 -0.4 381,469 - DDA3937_RS01720 0.13 -0.8 381,469 - +1.6 381,469 - DDA3937_RS01720 0.13 +1.3 381,469 - DDA3937_RS01720 0.13 +0.4 381,469 - DDA3937_RS01720 0.13 +1.2 381,469 - DDA3937_RS01720 0.13 -3.7 381,469 - DDA3937_RS01720 0.13 -1.4 381,470 + DDA3937_RS01720 0.14 +1.2 381,470 + DDA3937_RS01720 0.14 -0.4 381,471 - DDA3937_RS01720 0.14 -0.7 381,471 - DDA3937_RS01720 0.14 -1.8 381,471 - DDA3937_RS01720 0.14 -2.6 381,479 + DDA3937_RS01720 0.15 -2.7 381,483 - DDA3937_RS01720 0.15 -0.5 381,491 + +0.0 381,492 - DDA3937_RS01720 0.16 +0.6 381,506 - DDA3937_RS01720 0.18 -2.4 381,569 + DDA3937_RS01720 0.26 -2.3 381,584 + DDA3937_RS01720 0.28 -3.1 381,584 + DDA3937_RS01720 0.28 -0.7 381,621 - +0.6 381,623 + DDA3937_RS01720 0.32 -1.3 381,623 + DDA3937_RS01720 0.32 +0.0 381,623 + DDA3937_RS01720 0.32 +0.2 381,623 + DDA3937_RS01720 0.32 -0.4 381,624 - DDA3937_RS01720 0.33 +0.8 381,624 - DDA3937_RS01720 0.33 -1.4 381,624 - DDA3937_RS01720 0.33 -0.7 381,626 + DDA3937_RS01720 0.33 -2.4 381,626 + DDA3937_RS01720 0.33 -3.0 381,626 + DDA3937_RS01720 0.33 +1.9 381,626 + DDA3937_RS01720 0.33 -1.0 381,626 + DDA3937_RS01720 0.33 -1.9 381,626 + DDA3937_RS01720 0.33 -0.3 381,627 - DDA3937_RS01720 0.33 -1.1 381,657 + DDA3937_RS01720 0.37 +0.4 381,658 - DDA3937_RS01720 0.37 +0.2 381,658 - DDA3937_RS01720 0.37 +0.3 381,662 + DDA3937_RS01720 0.37 -0.9 381,669 + DDA3937_RS01720 0.38 -3.2 381,669 + DDA3937_RS01720 0.38 -0.7 381,671 + DDA3937_RS01720 0.38 -0.5 381,672 - DDA3937_RS01720 0.39 -0.2 381,672 - DDA3937_RS01720 0.39 +0.0 381,681 - DDA3937_RS01720 0.40 +2.2 381,730 + DDA3937_RS01720 0.46 +0.9 381,730 + DDA3937_RS01720 0.46 -1.0 381,730 + DDA3937_RS01720 0.46 -1.0 381,801 - DDA3937_RS01720 0.54 -3.0 381,846 + DDA3937_RS01720 0.60 -0.8 381,847 - DDA3937_RS01720 0.60 +0.2 381,847 - DDA3937_RS01720 0.60 -2.4 381,847 - DDA3937_RS01720 0.60 -3.0 381,878 + DDA3937_RS01720 0.64 +1.8 381,879 - DDA3937_RS01720 0.64 +0.9 381,879 - DDA3937_RS01720 0.64 +0.2 381,880 + DDA3937_RS01720 0.64 +0.1 381,880 + DDA3937_RS01720 0.64 +2.8 381,880 + DDA3937_RS01720 0.64 -0.4 381,880 + DDA3937_RS01720 0.64 -0.4 381,967 + DDA3937_RS01720 0.75 +0.4 381,967 + DDA3937_RS01720 0.75 +0.7 381,967 + DDA3937_RS01720 0.75 +1.1 381,983 + DDA3937_RS01720 0.77 +0.0 381,984 - DDA3937_RS01720 0.77 +0.8 382,021 + DDA3937_RS01720 0.82 +1.9 382,021 + DDA3937_RS01720 0.82 -0.7 382,022 - DDA3937_RS01720 0.82 -1.4 382,107 + +0.3 382,155 + +0.6 382,156 - -1.4 382,183 + -0.6 382,184 - +0.9 382,184 - +0.3 382,184 - +1.8 382,184 - -1.2 382,184 - +0.6 382,184 - -2.6 382,184 - -1.0 382,184 - +0.6 382,184 - -1.2 382,184 - +0.1 382,186 + +2.9 382,186 + -1.3 382,186 + +0.4 382,186 + +0.1 382,186 + -1.0 382,186 + +0.2 382,213 + +1.8 382,219 + -2.4 382,219 + +0.8 382,219 + +0.9 382,219 + +2.2 382,219 + +0.7 382,220 - +1.4 382,220 - -1.5 382,275 + -1.4 382,275 + -3.9 382,275 + +0.0 382,276 - -0.9 382,276 - -0.6 382,290 - -0.2 382,295 + -1.8 382,295 + +0.6 382,296 - -3.0 382,296 - -0.8 382,300 + +2.9 382,300 + -0.1 382,300 + -1.4 382,301 - -0.7 382,314 - -0.7 382,321 - +0.7 382,342 - -0.7 382,342 - +1.6 382,342 - -1.6 382,347 + -0.3 382,420 + -2.4 382,437 + DDA3937_RS01725 0.11 -3.9 382,475 + DDA3937_RS01725 0.16 -1.3 382,476 - DDA3937_RS01725 0.16 -1.2 382,495 + DDA3937_RS01725 0.19 +1.6 382,495 + DDA3937_RS01725 0.19 -0.1 382,495 + DDA3937_RS01725 0.19 -0.2 382,495 + DDA3937_RS01725 0.19 +0.4 382,495 + DDA3937_RS01725 0.19 -1.4 382,495 + DDA3937_RS01725 0.19 +2.2 382,495 + DDA3937_RS01725 0.19 +2.0 382,496 - DDA3937_RS01725 0.19 +1.3 382,496 - DDA3937_RS01725 0.19 -0.7 382,496 - DDA3937_RS01725 0.19 +2.4 382,496 - DDA3937_RS01725 0.19 -1.7 382,528 - DDA3937_RS01725 0.23 -0.1 382,528 - DDA3937_RS01725 0.23 +0.3 382,651 + DDA3937_RS01725 0.38 -2.1 382,651 + DDA3937_RS01725 0.38 -0.5 382,652 - DDA3937_RS01725 0.39 +1.6 382,652 - DDA3937_RS01725 0.39 +0.9 382,652 - DDA3937_RS01725 0.39 -2.5 382,652 - DDA3937_RS01725 0.39 +0.5 382,725 + DDA3937_RS01725 0.48 -1.2 382,771 + DDA3937_RS01725 0.54 +0.2 382,777 + DDA3937_RS01725 0.54 +1.1 382,777 + DDA3937_RS01725 0.54 -0.7 382,791 + DDA3937_RS01725 0.56 -2.6 382,792 - DDA3937_RS01725 0.56 -0.0 382,792 - DDA3937_RS01725 0.56 -1.6 383,038 + DDA3937_RS01725 0.87 -1.0 383,038 + DDA3937_RS01725 0.87 -2.0 383,038 + DDA3937_RS01725 0.87 -1.4 383,038 + DDA3937_RS01725 0.87 +0.7 383,038 + DDA3937_RS01725 0.87 +0.8 383,038 + DDA3937_RS01725 0.87 +2.0 383,038 + DDA3937_RS01725 0.87 +0.1 383,038 + DDA3937_RS01725 0.87 -0.3 383,038 + DDA3937_RS01725 0.87 -2.0 383,038 + DDA3937_RS01725 0.87 -2.1 383,039 - DDA3937_RS01725 0.88 -0.6 383,039 - DDA3937_RS01725 0.88 +0.0 383,039 - DDA3937_RS01725 0.88 +2.1 383,039 - DDA3937_RS01725 0.88 -0.7 383,039 - DDA3937_RS01725 0.88 +0.0 383,151 - +1.2 383,166 + -0.2 383,166 + -0.8 383,167 - -0.6
Or see this region's nucleotide sequence