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 | 49,905 | T→G | L28R (CTC→CGC) | folA → | type 3 dihydrofolate reductase |
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 | 356981 | 357576 | 596 | 3 [0] | [1] 2 | [lacA] | [lacA] |
* | * | ÷ | NZ_CP009273 | 428529 | 428567 | 39 | 2 [1] | [1] 3 | nrdR | transcriptional regulator NrdR |
* | * | ÷ | NZ_CP009273 | 879787 | 879802 | 16 | 2 [1] | [0] 2 | mdfA | multidrug efflux MFS transporter MdfA |
* | * | ÷ | NZ_CP009273 | 903029 | 903048 | 20 | 2 [1] | [0] 2 | ybjT | SDR family oxidoreductase |
* | * | ÷ | NZ_CP009273 | 1066281 | 1066285 | 5 | 2 [0] | [0] 2 | rutE | malonic semialdehyde reductase |
* | * | ÷ | NZ_CP009273 | 1172066 | 1172084 | 19 | 2 [1] | [1] 3 | [lolC]–[lolD] | [lolC],[lolD] |
* | * | ÷ | NZ_CP009273 | 1193243 | 1193270 | 28 | 2 [1] | [1] 2 | BW25113_RS05920 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1206663 | 1206671 | 9 | 2 [0] | [1] 2 | mcrA/BW25113_RS23640 | 5‑methylcytosine‑specific endonuclease McrA/isocitrate/isopropylmalate family dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1214934 | 1215024 | 91 | 3 [1] | [1] 2 | BW25113_RS06070/BW25113_RS25990 | hypothetical protein/autotransporter outer membrane beta‑barrel domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1225871 | 1225995 | 125 | 2 [0] | [1] 2 | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit |
* | * | ÷ | NZ_CP009273 | 1297652 | 1297657 | 6 | 2 [1] | [0] 2 | oppB | oligopeptide ABC transporter permease OppB |
* | * | ÷ | NZ_CP009273 | 1446140 | 1446163 | 24 | 2 [1] | [1] 3 | paaZ | phenylacetic acid degradation bifunctional protein PaaZ |
* | * | ÷ | NZ_CP009273 | 1524400 | 1524409 | 10 | 2 [1] | [1] 2 | BW25113_RS26145 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2097490 | 2097580 | 91 | 2 [1] | [1] 2 | wbbK | glycosyltransferase family 1 protein |
* | * | ÷ | NZ_CP009273 | 3629106 | 3629352 | 247 | 19 [0] | [1] 2 | [yhiM] | [yhiM] |
* | * | ÷ | NZ_CP009273 | 3629396 | 3629453 | 58 | 2 [1] | [0] 2 | yhiM/yhiN | DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase |
* | * | ÷ | NZ_CP009273 | 3629537 | 3629655 | 119 | 2 [0] | [1] 2 | [yhiN] | [yhiN] |
* | * | ÷ | NZ_CP009273 | 3629746 | 3630039 | 294 | 2 [1] | [1] 2 | yhiN | NAD(P)/FAD‑dependent oxidoreductase |
* | * | ÷ | NZ_CP009273 | 3630337 | 3630935 | 599 | 2 [0] | [1] 3 | [yhiN] | [yhiN] |
* | * | ÷ | NZ_CP009273 | 3631020 | 3631139 | 120 | 2 [0] | [0] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631229 | 3631703 | 475 | 2 [0] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3631794 | 3631942 | 149 | 2 [1] | [1] 3 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3632058 | 3632231 | 174 | 2 [1] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3632350 | 3632452 | 103 | 2 [1] | [1] 2 | pitA | inorganic phosphate transporter PitA |
* | * | ÷ | NZ_CP009273 | 3632574 | 3633914 | 1341 | 2 [0] | [0] 2 | uspB–uspA | uspB,uspA |
* | * | ÷ | NZ_CP009273 | 3633967 | 3634671 | 705 | 2 [0] | [0] 2 | BW25113_RS26225–[dtpB] | BW25113_RS26225,BW25113_RS26230,[dtpB] |
* | * | ÷ | NZ_CP009273 | 3634744 | 3634899 | 156 | 3 [1] | [0] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635022 | 3635307 | 286 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635461 | 3635613 | 153 | 2 [1] | [1] 2 | dtpB | dipeptide/tripeptide permease DtpB |
* | * | ÷ | NZ_CP009273 | 3635704 | 3635770 | 67 | 2 [1] | [1] 2 | [rsmJ] | [rsmJ] |
* | * | ÷ | NZ_CP009273 | 3636066 | 3636143 | 78 | 2 [1] | [1] 3 | rsmJ | 16S rRNA (guanine(1516)‑N(2))‑methyltransferase RsmJ |
* | * | ÷ | NZ_CP009273 | 3636706 | 3637157 | 452 | 2 [0] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637325 | 3637665 | 341 | 2 [1] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3637695 | 3638254 | 560 | 2 [1] | [1] 2 | prlC | oligopeptidase A |
* | * | ÷ | NZ_CP009273 | 3638499 | 3638605 | 107 | 2 [1] | [1] 3 | [prlC] | [prlC] |
* | * | ÷ | NZ_CP009273 | 3638679 | 3638835 | 157 | 2 [0] | [0] 2 | [rlmJ] | [rlmJ] |
* | * | ÷ | NZ_CP009273 | 3638926 | 3639299 | 374 | 2 [0] | [1] 2 | rlmJ | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
* | * | ÷ | NZ_CP009273 | 3639353 | 3639448 | 96 | 2 [1] | [0] 2 | rlmJ | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
* | * | ÷ | NZ_CP009273 | 3639595 | 3640091 | 497 | 2 [1] | [1] 2 | [gorA] | [gorA] |
* | * | ÷ | NZ_CP009273 | 3640156 | 3640271 | 116 | 2 [1] | [1] 2 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640343 | 3640412 | 70 | 2 [1] | [1] 3 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640636 | 3640786 | 151 | 2 [1] | [1] 2 | gorA | glutathione‑disulfide reductase |
* | * | ÷ | NZ_CP009273 | 3640877 | 3641036 | 160 | 2 [1] | [0] 2 | [gorA] | [gorA] |
* | * | ÷ | NZ_CP009273 | 3641131 | 3641298 | 168 | 2 [1] | [0] 2 | [dinQ] | [dinQ] |
* | * | ÷ | NZ_CP009273 | 3641356 | 3641431 | 76 | 2 [0] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3641449 | 3641584 | 136 | 2 [1] | [0] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3641634 | 3641644 | 11 | 2 [0] | [1] 2 | dinQ/arsR | hypothetical protein/As(III)‑sensing metalloregulatory transcriptional repressor ArsR |
* | * | ÷ | NZ_CP009273 | 3642116 | 3642729 | 614 | 2 [0] | [1] 2 | [arsR]–[arsB] | [arsR],[arsB] |
* | * | ÷ | NZ_CP009273 | 3642820 | 3643266 | 447 | 3 [0] | [1] 2 | arsB | arsenite/antimonite:H(+) antiporter ArsB |
* | * | ÷ | NZ_CP009273 | 3643342 | 3643429 | 88 | 2 [1] | [1] 2 | arsB | arsenite/antimonite:H(+) antiporter ArsB |
* | * | ÷ | NZ_CP009273 | 3643520 | 3643682 | 163 | 2 [1] | [1] 2 | [arsB]–[arsC] | [arsB],[arsC] |
* | * | ÷ | NZ_CP009273 | 3643789 | 3643800 | 12 | 2 [1] | [0] 2 | arsC | glutaredoxin‑dependent arsenate reductase |
* | * | ÷ | NZ_CP009273 | 3643967 | 3644056 | 90 | 2 [1] | [1] 2 | [arsC] | [arsC] |
* | * | ÷ | NZ_CP009273 | 3644147 | 3644420 | 274 | 2 [1] | [1] 2 | arsC/BW25113_RS18155 | glutaredoxin‑dependent arsenate reductase/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644511 | 3644557 | 47 | 2 [1] | [1] 3 | arsC/BW25113_RS18155 | glutaredoxin‑dependent arsenate reductase/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3644698 | 3645028 | 331 | 3 [1] | [1] 2 | BW25113_RS18155 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3645081 | 3645238 | 158 | 2 [1] | [1] 3 | BW25113_RS18155 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3645388 | 3646508–3645392 | 5–1121 | 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) | 42 (1.900) | 25/170 | 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 = | 8 (0.360) | 8 (0.450) | 7/138 | 0.8 | 62.8% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 3 (0.170) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 15 (0.690) | 11/168 | 0.6 | 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) | 27 (1.220) | 16/170 | 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 | = 3629105 | 0 (0.000) | 17 (0.780) | 13/168 | 0.4 | 100% | coding (905/1053 nt) | yhiM | DUF2776 domain‑containing protein |
? | NZ_CP009273 | 3645397 = | NA (NA) | pseudogene (747/747 nt) | BW25113_RS18155 | hypothetical protein | |||||
* | ? | NZ_CP009273 | = 4532507 | 9 (0.410) | 7 (0.350) | 6/152 | 1.0 | 26.4% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 31 (1.570) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |