mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 356951 | 357570 | 620 | 2 [1] | [0] 2 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 716379 | 716413 | 35 | 2 [0] | [0] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
| * | * | ÷ | NZ_CP009273 | 1037683 | 1037716 | 34 | 3 [1] | [1] 2 | etk | tyrosine‑protein kinase |
| * | * | ÷ | NZ_CP009273 | 1172386 | 1172430 | 45 | 2 [0] | [1] 2 | lolD | lipoprotein‑releasing ABC transporter ATP‑binding protein LolD |
| * | * | ÷ | NZ_CP009273 | 1282029 | 1282045 | 17 | 2 [1] | [0] 3 | narI/BW25113_RS23085 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| * | * | ÷ | NZ_CP009273 | 1631986 | 1632008 | 23 | 2 [1] | [0] 2 | gnsB | addiction module toxin, GnsA/GnsB family |
| * | * | ÷ | NZ_CP009273 | 2189903 | 2189909 | 7 | 2 [0] | [1] 4 | metG/BW25113_RS25680 | methionine‑‑tRNA ligase/WGR and DUF4132 domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 2622466 | 2622495 | 30 | 2 [1] | [1] 2 | [BW25113_RS25940] | [BW25113_RS25940] |
| * | * | ÷ | NZ_CP009273 | 3629247 | 3629714 | 468 | 26 [0] | [0] 2 | [yhiM]–[yhiN] | [yhiM],[yhiN] |
| * | * | ÷ | NZ_CP009273 | 3629781 | 3630376 | 596 | 2 [0] | [1] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
| * | * | ÷ | NZ_CP009273 | 3630403 | 3630531 | 129 | 2 [1] | [0] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
| * | * | ÷ | NZ_CP009273 | 3630607 | 3631613 | 1007 | 2 [0] | [1] 2 | [yhiN]–[pitA] | [yhiN],[pitA] |
| * | * | ÷ | NZ_CP009273 | 3631616 | 3632789 | 1174 | 2 [1] | [1] 2 | [pitA]–[uspB] | [pitA],[uspB] |
| * | * | ÷ | NZ_CP009273 | 3632803 | 3632898 | 96 | 2 [1] | [1] 2 | uspB | universal stress protein UspB |
| * | * | ÷ | NZ_CP009273 | 3632989 | 3633268 | 280 | 2 [1] | [1] 2 | [uspB] | [uspB] |
| * | * | ÷ | NZ_CP009273 | 3633291 | 3634246 | 956 | 2 [1] | [0] 2 | uspA–[dtpB] | uspA,BW25113_RS26225,BW25113_RS26230,[dtpB] |
| * | * | ÷ | NZ_CP009273 | 3634337 | 3634487 | 151 | 3 [1] | [1] 3 | dtpB | dipeptide/tripeptide permease DtpB |
| * | * | ÷ | NZ_CP009273 | 3634573 | 3636588 | 2016 | 2 [0] | [1] 2 | [dtpB]–[prlC] | [dtpB],rsmJ,[prlC] |
| * | * | ÷ | NZ_CP009273 | 3636644 | 3637045 | 402 | 2 [1] | [0] 2 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3637106 | 3637268 | 163 | 2 [0] | [1] 2 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3637359 | 3637708 | 350 | 2 [1] | [0] 2 | prlC | oligopeptidase A |
| * | * | ÷ | NZ_CP009273 | 3637769 | 3638564 | 796 | 2 [0] | [0] 2 | [prlC] | [prlC] |
| * | * | ÷ | NZ_CP009273 | 3638610 | 3639536 | 927 | 2 [0] | [1] 2 | [rlmJ] | [rlmJ] |
| * | * | ÷ | NZ_CP009273 | 3639654 | 3640017 | 364 | 2 [1] | [1] 2 | [gorA] | [gorA] |
| * | * | ÷ | NZ_CP009273 | 3640108 | 3640642 | 535 | 2 [1] | [0] 2 | gorA | glutathione‑disulfide reductase |
| * | * | ÷ | NZ_CP009273 | 3640706 | 3641958 | 1253 | 3 [1] | [0] 2 | [gorA]–[arsR] | [gorA],dinQ,[arsR] |
| * | * | ÷ | NZ_CP009273 | 3642001 | 3642530 | 530 | 2 [0] | [1] 2 | [arsR]–[arsB] | [arsR],[arsB] |
| * | * | ÷ | NZ_CP009273 | 3642538 | 3644731 | 2194 | 2 [1] | [1] 2 | [arsB]–[BW25113_RS18155] | [arsB],arsC,[BW25113_RS18155] |
| * | * | ÷ | NZ_CP009273 | 3644822 | 3645125 | 304 | 2 [1] | [0] 2 | BW25113_RS18155 | hypothetical protein |
| * | * | ÷ | NZ_CP009273 | 3645169 | 3646512–3645391 | 223–1344 | 2 [0] | [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) | 54 (2.870) | 27/168 | 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 = | 0 (0.000) | 11 (0.730) | 8/136 | 0.5 | 91.7% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 2 (0.130) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 0 (0.000) | 15 (0.990) | 12/136 | 0.2 | 93.8% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 2 (0.130) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 14 (0.750) | 10/166 | 0.5 | 78.0% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1972747 = | 4 (0.210) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_CP009273 | = 1903072 | 4 (0.210) | 18 (0.960) | 15/168 | 0.2 | 81.8% | 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) | 20 (1.060) | 14/168 | 0.3 | 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) | 22 (1.170) | 13/168 | 0.3 | 95.7% | 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) | 29 (1.560) | 16/166 | 0.2 | 100% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
| ? | NZ_CP009273 | = 3512441 | 0 (0.000) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
| * | ? | NZ_CP009273 | = 3629246 | 0 (0.000) | 25 (1.330) | 18/168 | 0.1 | 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 = | 2 (0.110) | 7 (0.420) | 7/150 | 0.7 | 61.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 7 (0.420) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 2 (0.110) | 6 (0.360) | 6/150 | 0.9 | 57.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 7 (0.420) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||