mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 49,765 | C→T | intergenic (+134/‑58) | kefC → / → folA | glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase |
| RA | 49,903 | T→G | D27E (GAT→GAG) | folA → | type 3 dihydrofolate reductase |
| RA | 50,279 | T→C | F153L (TTT→CTT) | folA → | type 3 dihydrofolate reductase |
| RA | 1,613,723 | G→C | G116A (GGC→GCC) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP009273 | 356976 | 357573 | 598 | 4 [3] | [3] 4 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 578897 | 579033 | 137 | 4 [2] | [3] 4 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
| * | * | ÷ | NZ_CP009273 | 613493 | 613561 | 69 | 7 [3] | [3] 4 | [entF] | [entF] |
| * | * | ÷ | NZ_CP009273 | 982708 | 982746 | 39 | 5 [2] | [3] 4 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
| * | * | ÷ | NZ_CP009273 | 1116572 | 1116606 | 35 | 5 [3] | [3] 4 | bssS/dinI | biofilm formation regulator BssS/DNA damage‑inducible protein I |
| * | * | ÷ | NZ_CP009273 | 1205059 | 1205074 | 16 | 18 [0] | [0] 31 | BW25113_RS06005 | phage tail protein |
| * | * | ÷ | NZ_CP009273 | 1207580 | 1207689 | 110 | 4 [3] | [3] 5 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
| * | * | ÷ | NZ_CP009273 | 1748979 | 1749084 | 106 | 4 [2] | [2] 4 | ydhY/fumD | ferredoxin‑like protein/fumarate hydratase FumD |
| * | * | ÷ | NZ_CP009273 | 1800499 | 1800537 | 39 | 4 [2] | [2] 4 | ydiY/pfkB | YdiY family protein/6‑phosphofructokinase II |
| * | * | ÷ | NZ_CP009273 | 2027336 | 2027453 | 118 | 4 [2] | [2] 4 | drpB/ompC | cell division protein DrpB/porin OmpC |
| * | * | ÷ | NZ_CP009273 | 2096858 | 2096907 | 50 | 5 [3] | [3] 4 | [wbbL]–[wbbK] | [wbbL],[wbbK] |
| * | * | ÷ | NZ_CP009273 | 2768272 | 2768341 | 70 | 6 [3] | [3] 5 | BW25113_RS13770 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 2975709 | 2975779 | 71 | 4 [2] | [3] 5 | araE/kduD | arabinose‑proton symporter AraE/2‑dehydro‑3‑deoxy‑D‑gluconate 5‑dehydrogenase KduD |
| * | * | ÷ | NZ_CP009273 | 2988540 | 2988671 | 132 | 4 [2] | [3] 5 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 3629488 | 3631696 | 2209 | 43 [0] | [2] 4 | yhiN–[pitA] | yhiN,[pitA] |
| * | * | ÷ | NZ_CP009273 | 3631732 | 3633354 | 1623 | 4 [3] | [3] 4 | [pitA]–uspB | [pitA],uspB |
| * | * | ÷ | NZ_CP009273 | 3633361 | 3634006 | 646 | 4 [3] | [3] 4 | uspA–[BW25113_RS26230] | uspA,[BW25113_RS26225],[BW25113_RS26230] |
| * | * | ÷ | NZ_CP009273 | 3634012 | 3638127 | 4116 | 4 [3] | [2] 4 | [BW25113_RS26225]–[prlC] | [BW25113_RS26225],[BW25113_RS26230],dtpB,rsmJ,[prlC] |
| * | * | ÷ | NZ_CP009273 | 3638188 | 3642299 | 4112 | 4 [2] | [3] 4 | [prlC]–[arsB] | [prlC],rlmJ,gorA,dinQ,arsR,[arsB] |
| * | * | ÷ | NZ_CP009273 | 3642385 | 3646524–3645398 | 3014–4140 | 4 [2] | [3] 4 | [arsB]–BW25113_RS18160 | [arsB],arsC,BW25113_RS18155,BW25113_RS18160 |
| * | * | ÷ | NZ_CP009273 | 4250367 | 4250399 | 33 | 4 [3] | [3] 5 | BW25113_RS21020 | DUF2713 domain‑containing protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | NA (NA) | 43 (1.280) | 22/164 | 0.3 | NA | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | NA (NA) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 1203246 = | 2 (0.060) | 24 (0.890) | 18/132 | 0.3 | 96.8% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 0 (0.000) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 2 (0.060) | 18 (0.670) | 16/132 | 0.4 | 95.7% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 0 (0.000) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 19 (0.570) | 13/162 | 0.8 | 100% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1972747 = | 0 (0.000) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 37 (1.100) | 22/164 | 0.3 | 100% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| ? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
| * | ? | NZ_CP009273 | 2282398 = | NA (NA) | 42 (1.250) | 20/164 | 0.4 | 100% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
| ? | NZ_CP009273 | = 3629487 | 0 (0.000) | intergenic (+234/+81) | yhiM/yhiN | DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase | |||||
| * | ? | NZ_CP009273 | 4532499 = | 0 (0.000) | 9 (0.300) | 6/146 | 1.6 | 90.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 2 (0.070) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 0 (0.000) | 14 (0.470) | 10/146 | 1.0 | 93.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 2 (0.070) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||