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 49,765 C→T intergenic (+134/‑58) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 49,912 G→T W30C (TGG→TGT)  folA → type 3 dihydrofolate reductase
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 243108 243124 17 2 [0] [0] 2 dinJ/yafL type II toxin‑antitoxin system antitoxin DinJ/C40 family peptidase
* * ÷ NZ_CP009273 295816 295819 4 2 [1] [0] 3 paoC aldehyde oxidoreductase molybdenum‑binding subunit PaoC
* * ÷ NZ_CP009273 356981 357572 592 2 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 579471 579483 13 2 [1] [1] 3 appY DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 608762 608822 61 3 [1] [1] 3 fes enterochelin esterase
* * ÷ NZ_CP009273 699701 699710 10 3 [0] [0] 2 nagE PTS N‑acetyl glucosamine transporter subunit IIABC
* * ÷ NZ_CP009273 716439 716481 43 2 [0] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 729579 729589 11 2 [0] [1] 4 BW25113_RS03630/BW25113_RS03635 hypothetical protein/RHS repeat protein
* * ÷ NZ_CP009273 768146 768203 58 2 [0] [1] 2 cydA cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 860886 860933 48 2 [1] [1] 2 moeA molybdopterin molybdotransferase MoeA
* * ÷ NZ_CP009273 903030 903053 24 2 [1] [1] 2 ybjT SDR family oxidoreductase
* * ÷ NZ_CP009273 982930 982971 42 2 [1] [1] 3 ompF/asnS porin OmpF/asparagine‑‑tRNA ligase
* * ÷ NZ_CP009273 987880 987912 33 2 [0] [1] 2 pepN aminopeptidase N
* * ÷ NZ_CP009273 993133 993187 55 2 [1] [1] 2 ssuE/elfA NADPH‑dependent FMN reductase/fimbrial protein
* * ÷ NZ_CP009273 1004495 1004570 76 2 [1] [1] 2 rlmKL bifunctional 23S rRNA (guanine(2069)‑N(7))‑methyltransferase RlmK/23S rRNA (guanine(2445)‑N(2))‑methyltransferase RlmL
* * ÷ NZ_CP009273 1088102 1088182 81 3 [1] [1] 2 pgaA/dgcT poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA/GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1098615 1098647 33 2 [1] [1] 2 csgD biofilm master transcriptional regulator CsgD
* * ÷ NZ_CP009273 1114580 1114660 81 3 [1] [1] 2 yceJ/BW25113_RS05515 cytochrome b/YceO family protein
* * ÷ NZ_CP009273 1144849 1144861 13 2 [0] [1] 2 fabH beta‑ketoacyl‑ACP synthase III
* * ÷ NZ_CP009273 1214867 1214868 2 2 [1] [0] 2 BW25113_RS06070/BW25113_RS25990 hypothetical protein/autotransporter outer membrane beta‑barrel domain‑containing protein
* * ÷ NZ_CP009273 1279894 1279904 11 2 [0] [0] 4 narH nitrate reductase subunit beta
* * ÷ NZ_CP009273 1320930 1320939 10 2 [1] [0] 2 yciQ/rluB DUF2207 domain‑containing protein/23S rRNA pseudouridine(2605) synthase RluB
* * ÷ NZ_CP009273 1386368 1386373 6 5 [1] [1] 2 pgrR DNA‑binding transcriptional regulator PgrR
* * ÷ NZ_CP009273 1424416 1424442 27 2 [1] [1] 2 stfR prophage tail fiber N‑terminal domain‑containing protein
* * ÷ NZ_CP009273 1498626 1498637 12 3 [1] [1] 2 insQ RNA‑guided endonuclease TnpB family protein
* * ÷ NZ_CP009273 2024912 2024922 11 3 [0] [1] 3 dcm DNA‑cytosine methyltransferase
* * ÷ NZ_CP009273 2027304 2027377 74 3 [1] [0] 4 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2050182 2050215 34 3 [1] [1] 2 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2300315 2300352 38 2 [1] [0] 2 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2359270 2359280 11 2 [0] [0] 2 ais/arnB lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase
* * ÷ NZ_CP009273 2463662 2463713 52 3 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2684957 2684969 13 2 [1] [1] 2 qseE/purL two component system sensor histidine kinase QseE/GlrK/phosphoribosylformylglycinamidine synthase
* * ÷ NZ_CP009273 2988605 2988628 24 2 [1] [0] 2 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3448792 3448818 27 3 [1] [0] 2 gspA/gspC type II secretion system protein GspA/type II secretion system protein GspC
* * ÷ NZ_CP009273 3463186 3463191 6 2 [0] [1] 2 chiA bifunctional chitinase/lysozyme
* * ÷ NZ_CP009273 3830118 3830127 10 2 [0] [1] 2 BW25113_RS26245/setC virulence RhuM family protein/sugar efflux transporter
* * ÷ NZ_CP009273 3837286 3837306 21 2 [0] [1] 3 adeQ/adeD adenine permease AdeQ/adenine deaminase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 287112NA (NA)32 (1.760) 19/168 0.1 91.4% intergenic (‑55/‑99) BW25113_RS01405/BW25113_RS01410 IS1‑like element IS1B family transposase/hypothetical protein
?NZ_CP009273 = 481508 3 (0.170)coding (292/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
* ? NZ_CP009273 360104 =NA (NA)11 (0.610) 7/168 0.9 45.8% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 13 (0.720)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 481499 =1 (0.060)15 (0.840) 13/166 0.3 93.8% coding (283/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
?NZ_CP009273 = 1046000 NA (NA)intergenic (+14/+419) BW25113_RS05135/cspH IS1‑like element IS1D family transposase/cold shock‑like protein CspH
* ? NZ_CP009273 = 1391494NA (NA)16 (0.890) 8/166 0.7 100% 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 = 19727510 (0.000)31 (1.710) 18/168 0.1 100% 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 4532499 =4 (0.220)8 (0.490) 8/150 0.6 54.1% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 10 (0.620)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA