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 | 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 | 356969 | 357580 | 612 | 3 [2] | [2] 3 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 428519 | 428545 | 27 | 7 [2] | [2] 3 | nrdR | transcriptional regulator NrdR |
| * | * | ÷ | NZ_CP009273 | 578969 | 578997 | 29 | 3 [2] | [2] 4 | BW25113_RS26085/appY | tail fiber assembly protein/DNA‑binding transcriptional activator AppY |
| * | * | ÷ | NZ_CP009273 | 716401 | 716486 | 86 | 4 [2] | [2] 3 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
| * | * | ÷ | NZ_CP009273 | 950000 | 950068 | 69 | 3 [2] | [2] 3 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| * | * | ÷ | NZ_CP009273 | 982677 | 982728 | 52 | 3 [2] | [2] 4 | ompF/asnS | porin OmpF/asparagine‑‑tRNA ligase |
| * | * | ÷ | NZ_CP009273 | 1087989 | 1088023 | 35 | 3 [2] | [2] 5 | pgaA/dgcT | poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 1193066 | 1193096 | 31 | 3 [2] | [2] 4 | BW25113_RS05920 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1207789 | 1207803 | 15 | 4 [2] | [2] 4 | BW25113_RS25985/BW25113_RS25535 | protein YmgK/hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1329154 | 1329164 | 11 | 3 [1] | [0] 8 | cysB/ymiA | HTH‑type transcriptional regulator CysB/YmiA family putative membrane protein |
| * | * | ÷ | NZ_CP009273 | 1459439 | 1459482 | 44 | 3 [2] | [2] 3 | BW25113_RS25580 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1576878 | 1576999 | 122 | 3 [2] | [2] 4 | ydeN/ydeO | sulfatase/acid stress response transcriptional regulator YdeO |
| * | * | ÷ | NZ_CP009273 | 1888102 | 1888115 | 14 | 3 [2] | [2] 3 | yoaB/yoaC | RidA family protein/DUF1889 family protein |
| * | * | ÷ | NZ_CP009273 | 2027327 | 2027374 | 48 | 3 [1] | [2] 3 | drpB/ompC | cell division protein DrpB/porin OmpC |
| * | * | ÷ | NZ_CP009273 | 2988612 | 2988628 | 17 | 3 [2] | [0] 4 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 3629488 | 3632094 | 2607 | 44 [2] | [2] 4 | yhiN–[pitA] | yhiN,[pitA] |
| * | * | ÷ | NZ_CP009273 | 3632126 | 3632385 | 260 | 3 [2] | [1] 3 | pitA | inorganic phosphate transporter PitA |
| * | * | ÷ | NZ_CP009273 | 3632423 | 3632535 | 113 | 3 [2] | [1] 3 | [pitA] | [pitA] |
| * | * | ÷ | NZ_CP009273 | 3632585 | 3633264 | 680 | 3 [2] | [2] 3 | uspB | uspB |
| * | * | ÷ | NZ_CP009273 | 3633323 | 3633876 | 554 | 4 [2] | [2] 3 | [uspA] | [uspA] |
| * | * | ÷ | NZ_CP009273 | 3634052 | 3634686 | 635 | 3 [2] | [2] 3 | [BW25113_RS26230]–[dtpB] | [BW25113_RS26230],[dtpB] |
| * | * | ÷ | NZ_CP009273 | 3634689 | 3636237 | 1549 | 3 [2] | [2] 3 | [dtpB]–[rsmJ] | [dtpB],[rsmJ] |
| * | * | ÷ | NZ_CP009273 | 3636250 | 3636530 | 281 | 3 [1] | [2] 3 | [rsmJ]–[prlC] | [rsmJ],[prlC] |
| * | * | ÷ | NZ_CP009273 | 3636584 | 3637117 | 534 | 3 [2] | [2] 3 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3637119 | 3638152 | 1034 | 3 [2] | [2] 3 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3638213 | 3641198 | 2986 | 3 [2] | [2] 3 | [prlC]–dinQ | [prlC],rlmJ,gorA,dinQ |
| * | * | ÷ | NZ_CP009273 | 3641367 | 3641560 | 194 | 3 [2] | [1] 3 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
| * | * | ÷ | NZ_CP009273 | 3641633 | 3641804 | 172 | 3 [2] | [2] 3 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
| * | * | ÷ | NZ_CP009273 | 3641822 | 3643413 | 1592 | 3 [2] | [2] 3 | arsR–[arsB] | arsR,[arsB] |
| * | * | ÷ | NZ_CP009273 | 3643464 | 3644716 | 1253 | 3 [2] | [2] 4 | [arsB]–[BW25113_RS18155] | [arsB],arsC,[BW25113_RS18155] |
| * | * | ÷ | NZ_CP009273 | 3644771 | 3646531–3645398 | 628–1761 | 3 [2] | [2] 3 | [BW25113_RS18155]–BW25113_RS18160 | [BW25113_RS18155],BW25113_RS18160 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | NA (NA) | 34 (1.230) | 23/166 | 0.2 | 49.3% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 35 (1.260) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 1203246 = | 0 (0.000) | 16 (0.720) | 14/134 | 0.3 | 88.9% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 4 (0.180) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 0 (0.000) | 14 (0.630) | 9/134 | 0.8 | 87.5% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 4 (0.180) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 15 (0.550) | 8/164 | 1.2 | 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 | 2 (0.070) | 31 (1.120) | 17/166 | 0.4 | 93.9% | 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 (1.510) | 22/166 | 0.2 | 95.5% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
| ? | NZ_CP009273 | = 3629487 | 2 (0.070) | intergenic (+234/+81) | yhiM/yhiN | DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase | |||||
| * | ? | NZ_CP009273 | 4532499 = | 0 (0.000) | 14 (0.570) | 12/148 | 0.6 | 82.3% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 6 (0.240) | 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 (0.570) | 10/148 | 0.8 | 82.3% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 6 (0.240) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||