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 = 287112NA (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 = 1046001NA (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 = 1391494NA (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 = 19727510 (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