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 | 481,310 | A→T | T32S (ACC→TCC) | acrR → | multidrug efflux transporter transcriptional repressor AcrR |
| 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 | 356981 | 357591 | 611 | 2 [0] | [1] 4 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 903013 | 903047 | 35 | 3 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
| * | * | ÷ | NZ_CP009273 | 950090 | 950171 | 82 | 2 [1] | [1] 2 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| * | * | ÷ | NZ_CP009273 | 982718 | 982726 | 9 | 2 [0] | [1] 2 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
| * | * | ÷ | NZ_CP009273 | 1158185 | 1158249 | 65 | 2 [1] | [1] 2 | lpoB | penicillin‑binding protein activator LpoB |
| * | * | ÷ | NZ_CP009273 | 1164343 | 1164363 | 21 | 4 [1] | [0] 3 | comR/bhsA | TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA |
| * | * | ÷ | NZ_CP009273 | 1193201 | 1193251 | 51 | 2 [1] | [1] 3 | BW25113_RS05920 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1206601 | 1206616 | 16 | 2 [0] | [1] 2 | mcrA | 5‑methylcytosine‑specific endonuclease McrA |
| * | * | ÷ | NZ_CP009273 | 1207509 | 1207538 | 30 | 2 [1] | [0] 3 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
| * | * | ÷ | NZ_CP009273 | 1207645 | 1207698 | 54 | 2 [1] | [0] 2 | iraM/BW25113_RS25985 | anti‑adapter protein IraM/protein YmgK |
| * | * | ÷ | NZ_CP009273 | 1214923 | 1214954 | 32 | 2 [1] | [1] 2 | BW25113_RS06070/BW25113_RS25990 | hypothetical protein/autotransporter outer membrane beta‑barrel domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 1275848 | 1275850 | 3 | 2 [0] | [0] 2 | narG | nitrate reductase subunit alpha |
| * | * | ÷ | NZ_CP009273 | 3575349 | 3577509–3576787 | 1439–2161 | 42 [0] | [1] 2 | [hcp]–[BW25113_RS17830] | [hcp],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 | 360104 = | NA (NA) | 34 (1.320) | 18/168 | 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 = | 5 (0.190) | 12 (0.580) | 9/136 | 0.6 | 82.7% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 1 (0.050) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 5 (0.190) | 12 (0.580) | 11/136 | 0.5 | 82.7% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 1 (0.050) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 7 (0.270) | 3/166 | 1.8 | 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) | 33 (1.280) | 22/168 | 0.2 | 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) | 42 (1.630) | 30/168 | 0.0 | 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 = | 6 (0.230) | 16 (0.700) | 10/150 | 0.6 | 58.9% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 17 (0.740) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 6 (0.230) | 13 (0.570) | 8/150 | 0.8 | 53.8% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 17 (0.740) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||