mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 50,280 | T→G | F153C (TTT→TGT) | folA → | type 3 dihydrofolate reductase |
| RA | 768,739 | C→T | A81V (GCT→GTT) | cydB → | cytochrome d ubiquinol oxidase subunit II |
| RA | 1,613,378 | T→C | M1A (GTG→GCG) † | marR → | multiple antibiotic resistance transcriptional regulator MarR |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP009273 | 295809 | 295826 | 18 | 2 [1] | [0] 2 | paoC | aldehyde oxidoreductase molybdenum‑binding subunit PaoC |
| * | * | ÷ | NZ_CP009273 | 356981 | 357593 | 613 | 3 [0] | [1] 2 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 1423733 | 1423748 | 16 | 2 [1] | [1] 2 | stfR | prophage tail fiber N‑terminal domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 2050181 | 2050198 | 18 | 2 [0] | [1] 2 | amn/yeeN | AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator |
| * | * | ÷ | NZ_CP009273 | 2505243 | 2505287 | 45 | 3 [1] | [1] 2 | mntH | Nramp family divalent metal transporter |
| * | * | ÷ | NZ_CP009273 | 3575349 | 3576258 | 910 | 30 [0] | [0] 2 | hcp | Hcp1 family type VI secretion system effector |
| * | * | ÷ | NZ_CP009273 | 3576349 | 3576351 | 3 | 2 [0] | [0] 2 | hcp | Hcp1 family type VI secretion system effector |
| * | * | ÷ | NZ_CP009273 | 3576442 | 3577493–3576787 | 346–1052 | 2 [0] | [1] 3 | [BW25113_RS17825]–[BW25113_RS17830] | [BW25113_RS17825],BW25113_RS17830,[BW25113_RS17830] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 224503 = | NA (NA) | 3 (0.140) | 3/156 | 1.8 | NA | noncoding (2258/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA |
| ? | NZ_CP009273 | 224528 = | NA (NA) | noncoding (2283/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | NA (NA) | 20 (0.860) | 13/170 | 0.5 | 41.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 28 (1.210) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | = 377145 | NA (NA) | 6 (0.290) | 5/152 | 1.3 | NA | coding (24/914 nt) | BW25113_RS01870 | IS3‑like element IS2 family transposase |
| ? | NZ_CP009273 | = 377199 | NA (NA) | coding (78/914 nt) | BW25113_RS01870 | IS3‑like element IS2 family transposase | |||||
| * | ? | NZ_CP009273 | = 725724 | NA (NA) | 4 (0.190) | 4/152 | 1.5 | NA | coding (686/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NZ_CP009273 | = 725738 | NA (NA) | coding (700/4194 nt) | rhsC | rhs element protein RhsC | |||||
| * | ? | NZ_CP009273 | 1203246 = | 15 (0.650) | 6 (0.320) | 6/138 | 1.0 | 33.2% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 12 (0.640) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 17 (0.740) | 9/168 | 0.8 | 94.5% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1972747 = | 1 (0.040) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 39 (1.680) | 23/170 | 0.1 | 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 | = 3575348 | 0 (0.000) | 30 (1.290) | 19/170 | 0.2 | 100% | coding (126/1179 nt) | hcp | Hcp1 family type VI secretion system effector |
| ? | NZ_CP009273 | 3576788 = | NA (NA) | coding (391/417 nt) | BW25113_RS17825 | YrhA family protein | |||||
| * | ? | NZ_CP009273 | 4532499 = | 7 (0.300) | 16 (0.770) | 14/152 | 0.3 | 62.4% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 13 (0.630) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 7 (0.300) | 11 (0.530) | 8/152 | 0.8 | 53.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 13 (0.630) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||