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 | 49,910 | T→G | W30G (TGG→GGG) | folA → | type 3 dihydrofolate reductase |
RA | 1,310,410 | A→G | intergenic (‑118/+263) | yciG ← / ← trpA | general stress protein/tryptophan synthase subunit alpha |
RA | 1,613,393 | A→T | D6V (GAT→GTT) | marR → | multiple antibiotic resistance transcriptional regulator MarR |
MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
RA | 3,511,988 | C→A | E146* (GAG→TAG) | aroK ← | shikimate kinase AroK |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 356981 | 357567 | 587 | 2 [0] | [0] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 380336 | 380361 | 26 | 2 [1] | [1] 2 | BW25113_RS01880/tauA | PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein |
* | * | ÷ | NZ_CP009273 | 766539 | 766571 | 33 | 2 [1] | [1] 2 | mngB/cydA | mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I |
* | * | ÷ | NZ_CP009273 | 772567 | 772615 | 49 | 3 [1] | [1] 2 | tolA | cell envelope integrity protein TolA |
* | * | ÷ | NZ_CP009273 | 806467 | 806485 | 19 | 2 [0] | [1] 2 | bioF | 8‑amino‑7‑oxononanoate synthase |
* | * | ÷ | NZ_CP009273 | 1071822 | 1071853 | 32 | 2 [0] | [1] 2 | putA | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
* | * | ÷ | NZ_CP009273 | 1213813 | 1213847 | 35 | 2 [1] | [1] 2 | pdeG | cyclic diguanylate phosphodiesterase |
* | * | ÷ | NZ_CP009273 | 1225960 | 1225993 | 34 | 2 [0] | [1] 2 | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit |
* | * | ÷ | NZ_CP009273 | 1227046 | 1227073 | 28 | 2 [1] | [1] 2 | umuC | DNA polymerase V catalytic protein |
* | * | ÷ | NZ_CP009273 | 1250165 | 1250171 | 7 | 3 [1] | [0] 2 | ycgV | autotransporter outer membrane beta‑barrel domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1275105 | 1275150 | 46 | 2 [1] | [1] 2 | narK/narG | nitrate transporter NarK/nitrate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1283088 | 1283098 | 11 | 2 [0] | [0] 2 | BW25113_RS06420/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase |
* | * | ÷ | NZ_CP009273 | 1358665 | 1358709 | 45 | 2 [1] | [1] 2 | puuB | gamma‑glutamylputrescine oxidase |
* | * | ÷ | NZ_CP009273 | 1481225 | 1481261 | 37 | 2 [0] | [1] 2 | hrpA/ydcF | ATP‑dependent RNA helicase HrpA/YdcF family protein |
* | * | ÷ | NZ_CP009273 | 1509345 | 1509455 | 111 | 2 [0] | [1] 2 | ydcV | ABC transporter permease |
* | * | ÷ | NZ_CP009273 | 1524378 | 1524392 | 15 | 2 [1] | [0] 2 | BW25113_RS07645/BW25113_RS26145 | RHS repeat protein/hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1566347 | 1566393 | 47 | 2 [1] | [1] 2 | gadB/pqqL | glutamate decarboxylase/insulinase family protein |
* | * | ÷ | NZ_CP009273 | 1585492 | 1585557 | 66 | 2 [1] | [1] 2 | hipA | type II toxin‑antitoxin system serine/threonine protein kinase toxin HipA |
* | * | ÷ | NZ_CP009273 | 1635027 | 1635032 | 6 | 2 [0] | [0] 3 | essD/ynfU | phage lysis protein EssD/putative zinc‑binding protein YnfU |
* | * | ÷ | NZ_CP009273 | 1698814 | 1698814 | 1 | 2 [0] | [0] 2 | blr | division septum protein Blr |
* | * | ÷ | NZ_CP009273 | 1703210 | 1703216 | 7 | 3 [1] | [0] 2 | rsxC | electron transport complex subunit RsxC |
* | * | ÷ | NZ_CP009273 | 1711036 | 1711059 | 24 | 2 [1] | [1] 2 | tyrS | tyrosine‑‑tRNA ligase |
* | * | ÷ | NZ_CP009273 | 1807125 | 1807130 | 6 | 2 [0] | [1] 2 | BW25113_RS09050 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 1807480 | 1807572 | 93 | 2 [1] | [1] 2 | BW25113_RS09050/cedA | hypothetical protein/cell division activator CedA |
* | * | ÷ | NZ_CP009273 | 1814514 | 1814514 | 1 | 2 [0] | [0] 2 | chbC | PTS N,N'‑diacetylchitobiose transporter subunit IIC |
* | * | ÷ | NZ_CP009273 | 1990340 | 1990390 | 51 | 2 [1] | [1] 2 | sdiA/yecC | transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC |
* | * | ÷ | NZ_CP009273 | 2100620 | 2100700 | 81 | 2 [1] | [1] 2 | wzy | O16 family O‑antigen polymerase |
* | * | ÷ | NZ_CP009273 | 2137151 | 2137164 | 14 | 2 [0] | [1] 3 | dgcE | diguanylate cyclase |
* | * | ÷ | NZ_CP009273 | 2337816 | 2337902 | 87 | 2 [1] | [1] 3 | yfaL/nrdA | AIDA‑I family autotransporter adhesin YfaL/EhaC/ribonucleoside‑diphosphate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 2462995 | 2463040 | 46 | 3 [1] | [1] 3 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2463131 | 2463172 | 42 | 2 [0] | [1] 3 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 2623017 | 2623079 | 63 | 2 [1] | [1] 2 | yfgG/yfgH | YfgG family protein/glycine zipper 2TM domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 2653535 | 2653562 | 28 | 2 [1] | [1] 3 | iscU | Fe‑S cluster assembly scaffold IscU |
* | * | ÷ | NZ_CP009273 | 2753702 | 2753744 | 43 | 2 [1] | [1] 2 | yfjI | YfjI family protein |
* | * | ÷ | NZ_CP009273 | 2877658 | 2877732 | 75 | 2 [0] | [1] 2 | casA/cas3 | type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3 |
* | * | ÷ | NZ_CP009273 | 2988548 | 2988599 | 52 | 3 [1] | [1] 3 | BW25113_RS14850/BW25113_RS26010 | response regulator transcription factor/hypothetical protein |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | = 287112 | NA (NA) | 10 (0.580) | 7/166 | 0.8 | 83.3% | intergenic (‑55/‑99) | BW25113_RS01405/BW25113_RS01410 | IS1‑like element IS1B family transposase/hypothetical protein |
? | NZ_CP009273 | 1903038 = | 2 (0.120) | intergenic (‑15/‑144) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein | |||||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 42 (2.450) | 22/166 | 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 | = 1046001 | NA (NA) | 14 (0.820) | 11/166 | 0.4 | 100% | intergenic (+15/+418) | BW25113_RS05135/cspH | IS1‑like element IS1D family transposase/cold shock‑like protein CspH |
? | NZ_CP009273 | = 1903046 | 0 (0.000) | intergenic (‑23/‑136) | mgrB/yobH | PhoP/PhoQ regulator MgrB/YobH family protein | |||||
* | ? | NZ_CP009273 | 1203246 = | 4 (0.230) | 17 (1.230) | 13/134 | 0.1 | 89.0% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 1 (0.070) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 12 (0.710) | 7/164 | 0.8 | 92.4% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
? | NZ_CP009273 | 1972747 = | 1 (0.060) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
* | ? | NZ_CP009273 | = 1972751 | 0 (0.000) | 18 (1.050) | 15/166 | 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 |