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 1,184,613 A→T I207N (ATC→AAC)  phoQ ← two‑component system sensor histidine kinase PhoQ
RA 1,613,627 T→A V84E (GTG→GAG)  marR → multiple antibiotic resistance transcriptional regulator MarR
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 356981 357574 594 5 [0] [1] 2 [lacA] [lacA]
* * ÷ NZ_CP009273 419798 419799 2 2 [0] [0] 2 acpH ACP phosphodiesterase
* * ÷ NZ_CP009273 518495 518573 79 3 [0] [1] 2 ybbP/rhsD ABC transporter permease/rhs element protein RhsD
* * ÷ NZ_CP009273 567352 567405 54 2 [1] [1] 2 ybcM helix‑turn‑helix transcriptional regulator
* * ÷ NZ_CP009273 578930 578967 38 2 [0] [1] 2 BW25113_RS26085/appY tail fiber assembly protein/DNA‑binding transcriptional activator AppY
* * ÷ NZ_CP009273 647590 647642 53 3 [1] [1] 2 citC/dpiB [citrate (pro‑3S)‑lyase] ligase/sensor histidine kinase DpiB
* * ÷ NZ_CP009273 674902 674935 34 2 [0] [1] 2 ybeT/ybeU tetratricopeptide repeat protein/DUF1266 domain‑containing protein
* * ÷ NZ_CP009273 699965 699976 12 3 [1] [0] 2 nagE PTS N‑acetyl glucosamine transporter subunit IIABC
* * ÷ NZ_CP009273 716363 716390 28 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 716470 716509 40 2 [1] [1] 2 BW25113_RS26090/kdpE leader peptide SpeFL/two‑component system response regulator KdpE
* * ÷ NZ_CP009273 717726 717741 16 2 [1] [0] 2 kdpD two‑component system sensor histidine kinase KdpD
* * ÷ NZ_CP009273 724410 724449 40 2 [1] [0] 2 kdpF/ybfA K(+)‑transporting ATPase subunit F/YbfA family protein
* * ÷ NZ_CP009273 748538 748541 4 2 [0] [1] 2 ybgD/gltA fimbrial protein/citrate synthase
* * ÷ NZ_CP009273 798942 798973 32 2 [1] [1] 2 [ybhJ] [ybhJ]
* * ÷ NZ_CP009273 859095 859104 10 4 [1] [0] 2 [fsa] [fsa]
* * ÷ NZ_CP009273 869178 869198 21 2 [1] [1] 3 pdeI EAL domain‑containing protein
* * ÷ NZ_CP009273 962671 962672 2 4 [0] [0] 2 msbA lipid A ABC transporter ATP‑binding protein/permease MsbA
* * ÷ NZ_CP009273 1007732 1007747 16 4 [1] [0] 2 pqiA membrane integrity‑associated transporter subunit PqiA
* * ÷ NZ_CP009273 1021179 1021230 52 2 [0] [1] 2 helD DNA helicase IV
* * ÷ NZ_CP009273 1028371 1028375 5 2 [0] [0] 2 hyaA hydrogenase 1 small subunit
* * ÷ NZ_CP009273 1098942 1098980 39 2 [1] [0] 2 csgD/csgB biofilm master transcriptional regulator CsgD/curli minor subunit CsgB
* * ÷ NZ_CP009273 1172143 1172253 111 3 [1] [1] 3 lolD lipoprotein‑releasing ABC transporter ATP‑binding protein LolD
* * ÷ NZ_CP009273 1192377 1192477 101 3 [1] [0] 3 ymfD class I SAM‑dependent methyltransferase
* * ÷ NZ_CP009273 1193061 1193144 84 2 [1] [1] 2 BW25113_RS05920 hypothetical protein
* * ÷ NZ_CP009273 1207318 1207327 10 2 [1] [1] 2 iraM anti‑adapter protein IraM
* * ÷ NZ_CP009273 1208037 1208059 23 3 [1] [1] 2 BW25113_RS25535 hypothetical protein
* * ÷ NZ_CP009273 1242683 1242693 11 2 [0] [0] 9 treA alpha,alpha‑trehalase
* * ÷ NZ_CP009273 1251605 1251637 33 2 [1] [1] 2 ycgV/ychF autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF
* * ÷ NZ_CP009273 1298412 1298440 29 2 [1] [1] 2 oppC oligopeptide ABC transporter permease OppC
* * ÷ NZ_CP009273 1320895 1320952 58 4 [0] [1] 2 [yciQ] [yciQ]
* * ÷ NZ_CP009273 1327760 1327760 1 2 [0] [0] 2 topA type I DNA topoisomerase
* * ÷ NZ_CP009273 1364410 1364419 10 5 [0] [1] 2 pspE/ycjM thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase
* * ÷ NZ_CP009273 1387385 1387399 15 2 [0] [1] 2 pgrR/mppA DNA‑binding transcriptional regulator PgrR/murein tripeptide ABC transporter substrate‑binding protein MppA
* * ÷ NZ_CP009273 1400055 1400109 55 2 [1] [1] 3 abgR/smrA LysR family transcriptional regulator/DNA endonuclease SmrA
* * ÷ NZ_CP009273 1453533 1453580 48 2 [1] [1] 2 paaC 3‑hydroxyacyl‑CoA dehydrogenase PaaC
* * ÷ NZ_CP009273 1459420 1459534 115 2 [1] [1] 3 BW25113_RS25580 BW25113_RS25580
* * ÷ NZ_CP009273 1485607 1485634 28 2 [1] [1] 2 cybB cytochrome b561
* * ÷ NZ_CP009273 1514291 1514323 33 2 [0] [1] 2 [curA] [curA]
* * ÷ NZ_CP009273 1521518 1521575 58 2 [0] [1] 2 yncH/BW25113_RS07645 YncH family protein/RHS repeat protein
* * ÷ NZ_CP009273 1524271 1524373 103 2 [1] [0] 2 BW25113_RS07645/BW25113_RS26145 RHS repeat protein/hypothetical protein
* * ÷ NZ_CP009273 1525929 1525956 28 2 [1] [1] 3 BW25113_RS07655 ISAs1 family transposase
* * ÷ NZ_CP009273 1540351 1540425 75 2 [1] [1] 2 yddL/yddG porin/aromatic amino acid efflux DMT transporter YddG
* * ÷ NZ_CP009273 1573630 1573722 93 2 [1] [1] 2 yddA/BW25113_RS25610 ABC transporter ATP‑binding protein/permease/protein YneP
* * ÷ NZ_CP009273 1610126 1610156 31 4 [1] [0] 2 yneK putative protein YneK
* * ÷ NZ_CP009273 1618996 1619053 58 2 [1] [1] 2 [ydeJ] [ydeJ]
* * ÷ NZ_CP009273 1621453 1621499 47 2 [1] [1] 2 dcp peptidyl‑dipeptidase Dcp
* * ÷ NZ_CP009273 1631872 1632010 139 2 [1] [1] 3 gnsB addiction module toxin, GnsA/GnsB family
* * ÷ NZ_CP009273 1633072 1633089 18 2 [1] [1] 2 cspI/rzpQ cold shock protein CspI/DUF2514 domain‑containing protein
* * ÷ NZ_CP009273 1634950 1635042 93 2 [1] [1] 4 essD/ynfU phage lysis protein EssD/putative zinc‑binding protein YnfU
* * ÷ NZ_CP009273 1635288 1635319 32 2 [0] [1] 3 ynfU/cspB putative zinc‑binding protein YnfU/cold shock‑like protein CspB
* * ÷ NZ_CP009273 1741246 1741254 9 2 [0] [1] 2 ydhR monooxygenase
* * ÷ NZ_CP009273 1751464 1751479 16 3 [1] [1] 2 pykF/lpp pyruvate kinase PykF/murein lipoprotein Lpp
* * ÷ NZ_CP009273 1783818 1783862 45 2 [1] [1] 2 aroH/hemP 3‑deoxy‑7‑phosphoheptulonate synthase AroH/hemin uptake protein HemP
* * ÷ NZ_CP009273 1807502 1807574 73 3 [1] [1] 2 BW25113_RS09050/cedA hypothetical protein/cell division activator CedA
* * ÷ NZ_CP009273 1809774 1809788 15 2 [1] [1] 3 katE catalase HPII
* * ÷ NZ_CP009273 1864853 1864892 40 2 [1] [1] 2 cdgI GGDEF domain‑containing protein
* * ÷ NZ_CP009273 1886961 1886991 31 3 [1] [1] 2 yoaA ATP‑dependent DNA helicase
* * ÷ NZ_CP009273 1905346 1905378 33 2 [1] [1] 3 yebQ MFS transporter
* * ÷ NZ_CP009273 1952557 1952615 59 2 [0] [1] 2 torY/cutC NapC/NirT family cytochrome c/copper homeostasis protein CutC
* * ÷ NZ_CP009273 1973036 1973104 69 3 [1] [1] 2 flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* * ÷ NZ_CP009273 2015784 2015794 11 2 [0] [0] 3 fliP flagellar type III secretion system pore protein FliP
* * ÷ NZ_CP009273 2027367 2027423 57 2 [1] [1] 2 drpB/ompC cell division protein DrpB/porin OmpC
* * ÷ NZ_CP009273 2042217 2042228 12 2 [1] [0] 2 yeeJ inverse autotransporter adhesin YeeJ
* * ÷ NZ_CP009273 2050125 2050269 145 2 [1] [1] 2 amn/yeeN AMP nucleosidase/YebC/PmpR family DNA‑binding transcriptional regulator
* * ÷ NZ_CP009273 2051091 2051131 41 2 [1] [1] 2 yeeN/BW25113_RS10360 YebC/PmpR family DNA‑binding transcriptional regulator/tRNA‑Asn
* * ÷ NZ_CP009273 2062036 2062082 47 2 [0] [1] 2 BW25113_RS10415/BW25113_RS24005 IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein
* * ÷ NZ_CP009273 2144491 2144494 4 2 [0] [0] 4 yegI/yegJ protein kinase YegI/DUF2314 domain‑containing protein
* * ÷ NZ_CP009273 2300312 2300381 70 3 [1] [1] 4 mqo/yojI malate dehydrogenase (quinone)/microcin J25 efflux ABC transporter YojI
* * ÷ NZ_CP009273 2359194 2359210 17 3 [0] [0] 2 ais/arnB lipopolysaccharide core heptose(II)‑phosphate phosphatase Ais/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase
* * ÷ NZ_CP009273 2449501 2449517 17 2 [0] [1] 3 yfcV/sixA fimbrial protein/phosphohistidine phosphatase SixA
* * ÷ NZ_CP009273 2462911 2462924 14 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463196 2463249 54 2 [1] [0] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2463656 2463794 139 2 [1] [1] 2 BW25113_RS12270 hypothetical protein
* * ÷ NZ_CP009273 2505237 2505285 49 3 [0] [1] 2 mntH Nramp family divalent metal transporter
* * ÷ NZ_CP009273 2622404 2622470 67 2 [1] [0] 2 pdeF/BW25113_RS25940 cyclic‑guanylate‑specific phosphodiesterase PdeF/hypothetical protein
* * ÷ NZ_CP009273 2622536 2622540 5 2 [0] [1] 2 BW25113_RS25940 hypothetical protein
* * ÷ NZ_CP009273 2623009 2623027 19 2 [1] [1] 2 yfgG/yfgH YfgG family protein/glycine zipper 2TM domain‑containing protein
* * ÷ NZ_CP009273 2768270 2768282 13 2 [1] [0] 4 BW25113_RS13770 hypothetical protein
* * ÷ NZ_CP009273 2877746 2877788 43 2 [1] [0] 3 casA/cas3 type I‑E CRISPR‑associated protein Cse1/CasA/CRISPR‑associated helicase/endonuclease Cas3
* * ÷ NZ_CP009273 2988508 2988651 144 2 [1] [1] 3 BW25113_RS14850/BW25113_RS26010 response regulator transcription factor/hypothetical protein
* * ÷ NZ_CP009273 3262628 3262746 119 2 [0] [1] 2 yhaC YhaC family protein
* * ÷ NZ_CP009273 3354473 3354481 9 2 [0] [0] 2 gltD/gltF glutamate synthase subunit GltD/DUF1120 domain‑containing protein
* * ÷ NZ_CP009273 3591174 3591186 13 2 [0] [1] 2 livK/panM high‑affinity branched‑chain amino acid ABC transporter substrate‑binding protein LivK/aspartate 1‑decarboxylase autocleavage activator PanM
* * ÷ NZ_CP009273 3790424 3790457 34 3 [1] [0] 2 waaL O‑antigen ligase
* * ÷ NZ_CP009273 3790495 3790549 55 2 [0] [1] 2 waaL O‑antigen ligase

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)61 (3.750) 34/168 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 = 1391494NA (NA)12 (0.750) 6/166 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 (1.110) 13/168 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
* ? NZ_CP009273 4532499 =2 (0.120)8 (0.550) 8/150 0.5 50.3% intergenic (+49/‑433) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 4532813 = 14 (0.970)intergenic (+363/‑119) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
* ? NZ_CP009273 = 45325072 (0.120)8 (0.550) 7/150 0.6 50.3% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 14 (0.970)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA