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 49,791 G→A intergenic (+160/‑32) kefC → / → folA glutathione‑regulated potassium‑efflux system protein KefC/type 3 dihydrofolate reductase
RA 1,210,188 C→T L248L (CTG→CTA)  bluF ← blue light‑responsive regulator BluF
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
RA 4,267,830 G→C G145A (GGC→GCC)  soxR → redox‑sensitive transcriptional activator SoxR

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 80511 80592 82 2 [1] [1] 2 leuL/leuO leu operon leader peptide/transcriptional regulator LeuO
* * ÷ NZ_CP009273 233698 233708 11 2 [1] [0] 2 BW25113_RS01085/BW25113_RS01090 tRNA‑Asp/lipoprotein
* * ÷ NZ_CP009273 235100 235120 21 3 [1] [1] 2 BW25113_RS01095 hypothetical protein
* * ÷ NZ_CP009273 356969 357574 606 3 [1] [1] 3 [lacA] [lacA]
* * ÷ NZ_CP009273 380404 380455 52 2 [0] [1] 2 BW25113_RS01880/tauA PIG‑L family deacetylase/taurine ABC transporter substrate‑binding protein
* * ÷ NZ_CP009273 476532 476570 39 2 [1] [1] 2 tomB/acrB Hha toxicity modulator TomB/efflux RND transporter permease AcrB
* * ÷ NZ_CP009273 578979 579046 68 4 [1] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 716401 716436 36 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 748348 748395 48 3 [0] [0] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 766324 766374 51 2 [0] [1] 2 mngB/cydA mannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
* * ÷ NZ_CP009273 880819 880832 14 3 [0] [1] 2 ybjI 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase
* * ÷ NZ_CP009273 930676 930686 11 2 [1] [0] 2 ftsK DNA translocase FtsK
* * ÷ NZ_CP009273 1001622 1001647 26 2 [0] [1] 2 zapC cell division protein ZapC
* * ÷ NZ_CP009273 1098968 1098994 27 2 [1] [1] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1114585 1114621 37 3 [1] [1] 2 yceJ/BW25113_RS05515 cytochrome b/YceO family protein
* * ÷ NZ_CP009273 1164393 1164439 47 2 [1] [0] 2 comR/bhsA TetR family copper‑responsive transcriptional repressor ComR/multiple stress resistance protein BhsA
* * ÷ NZ_CP009273 1193083 1193098 16 2 [1] [0] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1193181 1193213 33 2 [0] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1209586 1209591 6 2 [0] [0] 3 bluR/bluF DNA‑binding transcriptional repressor BluR/blue light‑responsive regulator BluF
* * ÷ NZ_CP009273 1275142 1275150 9 3 [0] [0] 2 narK/narG nitrate transporter NarK/nitrate reductase subunit alpha
* * ÷ NZ_CP009273 1341132 1341201 70 2 [1] [1] 2 [BW25113_RS25050] [BW25113_RS25050]
* * ÷ NZ_CP009273 1362454 1362542 89 2 [1] [1] 2 pspA phage shock protein PspA
* * ÷ NZ_CP009273 1369673 1369682 10 4 [1] [1] 2 ycjQ zinc‑binding alcohol dehydrogenase
* * ÷ NZ_CP009273 1380784 1380864 81 2 [1] [1] 2 [ycjF] [ycjF]
* * ÷ NZ_CP009273 1452927 1452947 21 2 [1] [0] 2 paaG 2‑(1,2‑epoxy‑1,2‑dihydrophenyl)acetyl‑CoA isomerase PaaG
* * ÷ NZ_CP009273 1521134 1521139 6 2 [0] [0] 2 yncG/yncH glutathione S‑transferase family protein/YncH family protein
* * ÷ NZ_CP009273 1524363 1524420 58 2 [1] [1] 2 [BW25113_RS26145] [BW25113_RS26145]
* * ÷ NZ_CP009273 1540396 1540460 65 2 [1] [1] 3 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1565625–1565652 1566004–1565662 11–380 2 [1] [1] 2 gadB glutamate decarboxylase
* * ÷ NZ_CP009273 1566573 1566634 62 2 [1] [1] 3 gadB/pqqL glutamate decarboxylase/insulinase family protein
* * ÷ NZ_CP009273 1580924 1580984 61 2 [1] [1] 2 ydeP/ydeQ acid resistance putative oxidoreductase YdeP/fimbrial protein
* * ÷ NZ_CP009273 1645987 1645997 11 4 [1] [0] 3 BW25113_RS25635 tyrosine‑type recombinase/integrase
* * ÷ NZ_CP009273 1724107 1724110 4 2 [0] [1] 3 lhr ATP‑dependent helicase
* * ÷ NZ_CP009273 1748951 1749069 119 2 [1] [1] 2 ydhY/fumD ferredoxin‑like protein/fumarate hydratase FumD
* * ÷ NZ_CP009273 1760095 1760128 34 2 [1] [1] 2 ydiJ FAD‑binding and (Fe‑S)‑binding domain‑containing protein
* * ÷ NZ_CP009273 1783828 1783846 19 2 [1] [1] 3 aroH/hemP 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP
* * ÷ NZ_CP009273 1799372 1799406 35 3 [1] [1] 2 espL1/BW25113_RS09005 type III secretion system effector EspL1/hypothetical protein
* * ÷ NZ_CP009273 1806965 1807007 43 3 [1] [1] 2 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1807072 1807107 36 2 [1] [1] 2 BW25113_RS09050 hypothetical protein
* * ÷ NZ_CP009273 1826462 1826472 11 3 [0] [0] 3 astC/xthA succinylornithine/acetylornithine transaminase/exodeoxyribonuclease III
* * ÷ NZ_CP009273 1875414 1875442 29 2 [0] [1] 2 dmlR DNA‑binding transcriptional regulator DmlR
* * ÷ NZ_CP009273 1882257 1882268 12 2 [0] [0] 5 rnd/fadD ribonuclease D/long‑chain‑fatty‑acid‑‑CoA ligase FadD
* * ÷ NZ_CP009273 1919605 1919615 11 2 [0] [0] 3 holE/yobB DNA polymerase III subunit theta/carbon‑nitrogen hydrolase family protein
* * ÷ NZ_CP009273 1978840 1978857 18 2 [1] [1] 2 araF arabinose ABC transporter substrate‑binding protein AraF
* * ÷ NZ_CP009273 1997263 1997271 9 3 [0] [0] 2 fliC/fliD H48 family flagellin FliC/flagellar filament capping protein FliD
* * ÷ NZ_CP009273 2027033 2027114 82 2 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2115970 2116003 34 2 [1] [0] 3 cpsG colanic acid biosynthesis phosphomannomutase CpsG
* * ÷ NZ_CP009273 2144482 2144532 51 3 [1] [1] 2 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2161950 2161960 11 2 [0] [1] 2 BW25113_RS10880/yegS hypothetical protein/lipid kinase YegS
* * ÷ NZ_CP009273 2300351 2300377 27 2 [1] [0] 2 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2370767 2370814 48 2 [1] [1] 4 menH 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
* * ÷ NZ_CP009273 2463700 2463778 79 3 [1] [1] 3 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2623000 2623040 41 2 [1] [1] 3 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2687535 2687552 18 2 [1] [1] 2 purL phosphoribosylformylglycinamidine synthase
* * ÷ NZ_CP009273 2768281 2768310 30 2 [0] [1] 2 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2772487 2772492 6 2 [0] [1] 2 ypjA adhesin‑like autotransporter YpjA/EhaD
* * ÷ NZ_CP009273 2988490 2988641 152 2 [1] [0] 3 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3112496 3112515 20 2 [0] [1] 4 sslE/glcA lipoprotein metalloprotease SslE/glycolate permease GlcA
* * ÷ NZ_CP009273 3178647 3178691 45 2 [1] [1] 2 ubiK/ygiL ubiquinone biosynthesis accessory factor UbiK/fimbrial‑like protein
* * ÷ NZ_CP009273 3262563 3262615 53 3 [1] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3787086 3787096 11 2 [1] [1] 3 yibB/rfaD protein YibB/ADP‑glyceromanno‑heptose 6‑epimerase
* * ÷ NZ_CP009273 3996657 3996667 11 3 [0] [1] 6 rarD EamA family transporter RarD
* * ÷ NZ_CP009273 4037408 4037437 30 4 [1] [0] 2 dsbA/yihF thiol:disulfide interchange protein DsbA/YdgA family protein
* * ÷ NZ_CP009273 4272715 4272748 34 2 [1] [0] 2 espX5 T3SS effector pentapeptide repeat protein EspX5

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)22 (1.360) 16/168 0.1 44.9% intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 27 (1.670)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 1203246 =8 (0.490)5 (0.380) 5/136 0.8 46.6% coding (290/630 nt) BW25113_RS05990 hypothetical protein
?NZ_CP009273 1205075 = 5 (0.380)coding (40/540 nt) BW25113_RS06005 phage tail protein
* ? NZ_CP009273 = 1391494NA (NA)14 (0.870) 9/166 0.5 100% 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 = 19727511 (0.060)15 (0.930) 12/168 0.3 93.8% 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)17 (1.050) 8/168 0.6 100% pseudogene (3/2532 nt) yejO autotransporter YejO
?NZ_CP009273 3512437 = 0 (0.000)intergenic (‑14/+387) aroK/hofQ shikimate kinase AroK/DNA uptake porin HofQ
* ? NZ_CP009273 = 2283591NA (NA)13 (0.810) 10/166 0.4 100% 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