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→A | D27E (GAT→GAA) | folA → | type 3 dihydrofolate reductase |
| RA | 49,910 | T→A | W30R (TGG→AGG) | folA → | type 3 dihydrofolate reductase |
| JC | 1,613,631 | Δ3 bp | coding (255‑257/435 nt) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | 3,632,461 | T→G | L487R (CTT→CGT) | pitA → | inorganic phosphate transporter PitA |
| 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 | 356981 | 357567 | 587 | 4 [0] | [0] 4 | lacA | galactoside O‑acetyltransferase |
| * | * | ÷ | NZ_CP009273 | 579014 | 579053 | 40 | 2 [1] | [0] 2 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
| * | * | ÷ | NZ_CP009273 | 656818 | 656829 | 12 | 2 [0] | [1] 3 | ybeF | YbeF family transcriptional regulator |
| * | * | ÷ | NZ_CP009273 | 716424 | 716481 | 58 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
| * | * | ÷ | NZ_CP009273 | 1091297 | 1091306 | 10 | 2 [0] | [1] 2 | [BW25113_RS05355]–[BW25113_RS05360] | [BW25113_RS05355],[BW25113_RS05360] |
| * | * | ÷ | NZ_CP009273 | 1164362 | 1164427 | 66 | 2 [1] | [1] 3 | comR/bhsA | TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA |
| * | * | ÷ | NZ_CP009273 | 1192452 | 1192489 | 38 | 2 [1] | [1] 2 | ymfD | class I SAM‑dependent methyltransferase |
| * | * | ÷ | NZ_CP009273 | 1193084 | 1193144 | 61 | 3 [0] | [0] 2 | BW25113_RS05920 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1193262 | 1193312 | 51 | 2 [0] | [1] 2 | BW25113_RS05920 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1206767 | 1206774 | 8 | 2 [0] | [1] 2 | mcrA/BW25113_RS23640 | 5‑methylcytosine‑specific endonuclease McrA/isocitrate/isopropylmalate family dehydrogenase |
| * | * | ÷ | NZ_CP009273 | 1807468 | 1807552 | 85 | 2 [1] | [1] 2 | BW25113_RS09050/cedA | hypothetical protein/cell division activator CedA |
| * | * | ÷ | NZ_CP009273 | 2027104 | 2027124 | 21 | 2 [1] | [0] 2 | drpB/ompC | cell division protein DrpB/porin OmpC |
| * | * | ÷ | NZ_CP009273 | 2462910 | 2462944 | 35 | 3 [1] | [1] 2 | BW25113_RS12270 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 2463141 | 2463180 | 40 | 2 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 2463618 | 2463665 | 48 | 2 [1] | [0] 2 | BW25113_RS12270 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 2877661 | 2877688 | 28 | 2 [1] | [1] 2 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | NA (NA) | 100 (3.350) | 33/164 | 0.0 | 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 = | 7 (0.230) | 16 (0.670) | 9/132 | 0.8 | 78.8% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 3 (0.120) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 7 (0.230) | 17 (0.710) | 12/132 | 0.5 | 79.8% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 3 (0.120) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 19 (0.640) | 11/162 | 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) | 28 (0.940) | 22/164 | 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 | 4532499 = | 2 (0.070) | 10 (0.380) | 6/146 | 1.4 | 84.1% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 2 (0.080) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 2 (0.070) | 5 (0.190) | 5/146 | 1.6 | 72.6% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 2 (0.080) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||