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 | 1,613,576 | A→C | D67A (GAC→GCC) | 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 | 233698 | 233720 | 23 | 2 [1] | [0] 2 | BW25113_RS01085/BW25113_RS01090 | tRNA‑Asp/lipoprotein |
| * | * | ÷ | NZ_CP009273 | 356981 | 357570 | 590 | 7 [0] | [1] 2 | lacA | galactoside O‑acetyltransferase |
| * | * | ÷ | NZ_CP009273 | 1193192 | 1193247 | 56 | 4 [0] | [0] 2 | BW25113_RS05920 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 1207675 | 1207735 | 61 | 4 [0] | [1] 2 | [BW25113_RS25985] | [BW25113_RS25985] |
| * | * | ÷ | NZ_CP009273 | 1573658 | 1573722 | 65 | 2 [1] | [1] 2 | yddA/BW25113_RS25610 | ABC transporter ATP‑binding protein/permease/protein YneP |
| * | * | ÷ | NZ_CP009273 | 1635248 | 1635282 | 35 | 4 [1] | [1] 2 | ynfU/cspB | putative zinc‑binding protein YnfU/cold shock‑like protein CspB |
| * | * | ÷ | NZ_CP009273 | 1748961 | 1749036 | 76 | 2 [1] | [0] 2 | ydhY/fumD | ferredoxin‑like protein/fumarate hydratase FumD |
| * | * | ÷ | NZ_CP009273 | 2100171 | 2100191 | 21 | 2 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
| * | * | ÷ | NZ_CP009273 | 3247147 | 3247151 | 5 | 3 [0] | [0] 2 | yhaJ | DNA‑binding transcriptional regulator YhaJ |
| * | * | ÷ | NZ_CP009273 | 3280656 | 3280662 | 7 | 3 [1] | [0] 2 | agaI/yraH | galactosamine‑6‑phosphate isomerase/fimbrial protein |
| * | * | ÷ | NZ_CP009273 | 3629247 | 3630389 | 1143 | 27 [0] | [1] 2 | [yhiM]–[yhiN] | [yhiM],[yhiN] |
| * | * | ÷ | NZ_CP009273 | 3630535 | 3633841 | 3307 | 2 [0] | [1] 3 | [yhiN]–[uspA] | [yhiN],pitA,uspB,[uspA] |
| * | * | ÷ | NZ_CP009273 | 3633912 | 3634197 | 286 | 2 [0] | [1] 2 | BW25113_RS26225–BW25113_RS26230 | BW25113_RS26225,BW25113_RS26230 |
| * | * | ÷ | NZ_CP009273 | 3634200 | 3634576 | 377 | 2 [1] | [1] 2 | [dtpB] | [dtpB] |
| * | * | ÷ | NZ_CP009273 | 3634667 | 3634762 | 96 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
| * | * | ÷ | NZ_CP009273 | 3634853 | 3635137 | 285 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
| * | * | ÷ | NZ_CP009273 | 3635200 | 3635501 | 302 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
| * | * | ÷ | NZ_CP009273 | 3635592 | 3635848 | 257 | 2 [1] | [1] 2 | [dtpB]–[rsmJ] | [dtpB],[rsmJ] |
| * | * | ÷ | NZ_CP009273 | 3636005 | 3636650 | 646 | 3 [1] | [1] 2 | [rsmJ]–[prlC] | [rsmJ],[prlC] |
| * | * | ÷ | NZ_CP009273 | 3636701 | 3637560 | 860 | 2 [1] | [1] 2 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3637605 | 3638054 | 450 | 2 [1] | [1] 2 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3638178 | 3639220 | 1043 | 2 [1] | [1] 2 | [prlC]–[rlmJ] | [prlC],[rlmJ] |
| * | * | ÷ | NZ_CP009273 | 3639248 | 3641046 | 1799 | 2 [1] | [0] 2 | [rlmJ]–gorA | [rlmJ],gorA |
| * | * | ÷ | NZ_CP009273 | 3641137 | 3641217 | 81 | 2 [0] | [0] 2 | [dinQ] | [dinQ] |
| * | * | ÷ | NZ_CP009273 | 3641308 | 3641383 | 76 | 3 [1] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
| * | * | ÷ | NZ_CP009273 | 3641470 | 3641484 | 15 | 2 [1] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
| * | * | ÷ | NZ_CP009273 | 3641570 | 3642448 | 879 | 2 [1] | [1] 2 | arsR–[arsB] | arsR,[arsB] |
| * | * | ÷ | NZ_CP009273 | 3642491 | 3644069 | 1579 | 2 [1] | [1] 2 | [arsB]–arsC | [arsB],arsC |
| * | * | ÷ | NZ_CP009273 | 3644179 | 3644891 | 713 | 3 [1] | [1] 2 | [BW25113_RS18155] | [BW25113_RS18155] |
| * | * | ÷ | NZ_CP009273 | 3644992 | 3646519–3645390 | 399–1528 | 2 [1] | [1] 2 | [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) | 80 (4.030) | 35/166 | 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 = | 10 (0.500) | 11 (0.690) | 7/134 | 0.7 | 66.6% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 3 (0.190) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 5 (0.260) | 5/164 | 1.3 | 83.5% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1972747 = | 1 (0.050) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_CP009273 | = 1391495 | NA (NA) | 10 (0.500) | 8/166 | 0.8 | 100% | intergenic (+146/‑127) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1903069 = | 0 (0.000) | intergenic (‑46/‑113) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein | |||||
| * | ? | NZ_CP009273 | = 1903072 | 0 (0.000) | 20 (1.010) | 13/166 | 0.4 | 100% | intergenic (‑49/‑110) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein |
| ? | NZ_CP009273 | = 2096424 | NA (NA) | intergenic (‑68/+3) | BW25113_RS10605/wbbL | IS5‑like element IS5 family transposase/N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL | |||||
| * | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 19 (0.960) | 16/166 | 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 | 2282398 = | NA (NA) | 17 (0.860) | 10/166 | 0.6 | 94.4% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
| ? | NZ_CP009273 | 3512437 = | 1 (0.050) | intergenic (‑14/+387) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
| * | ? | NZ_CP009273 | = 2283591 | NA (NA) | 21 (1.070) | 16/164 | 0.2 | 95.5% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
| ? | NZ_CP009273 | = 3512441 | 1 (0.050) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
| * | ? | NZ_CP009273 | = 3629246 | 0 (0.000) | 27 (1.360) | 14/166 | 0.3 | 100% | coding (1046/1053 nt) | yhiM | DUF2776 domain‑containing protein |
| ? | NZ_CP009273 | 3645396 = | NA (NA) | pseudogene (746/747 nt) | BW25113_RS18155 | hypothetical protein | |||||
| * | ? | NZ_CP009273 | 4532499 = | 4 (0.200) | 9 (0.510) | 9/148 | 0.6 | 57.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 10 (0.570) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 4 (0.200) | 8 (0.450) | 7/148 | 0.8 | 54.1% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 10 (0.570) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||