breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 44,293 Δ1 bp 100% intergenic (+124/‑367) oprD_1 → / → czcR_2 Porin D/Transcriptional activator protein CzcR
RA 65,165 G→A 6.0% N31N (AAC→AAT)  CJ019_00068 ← hypothetical protein
RA 120,975 Δ1 bp 100% intergenic (+272/+100) polA → / ← engB DNA polymerase I/putative GTP‑binding protein EngB
RA 179,484 T→C 100% C316R (TGC→CGC)  CJ019_00182 → hypothetical protein
RA 606,939 C→T 6.7% R98H (CGC→CAC)  dxs ← 1‑deoxy‑D‑xylulose‑5‑phosphate synthase
RA 740,674 T→G 50.5% L38R (CTG→CGG)  CJ019_00704 → hypothetical protein
RA 763,776 T→G 28.2% V137G (GTC→GGC)  thrC_1 → Threonine synthase
RA 828,159 C→T 6.4% A324T (GCC→ACC)  CJ019_00791 ← putative sulfate transporter
RA 868,330 T→G 43.9% intergenic (+19/+27) loiP → / ← mneA Metalloprotease LoiP/Putative manganese exporter
RA 907,674 G→A 8.0% A445A (GCG→GCA)  fruA → PTS system fructose‑specific EIIB'BC component
RA 1,451,862 G→A 8.7% P263S (CCG→TCG)  algA_1 ← Alginate biosynthesis protein AlgA
RA 1,529,589 C→T 10.2% L57L (CTG→TTG)  CJ019_01442 → hypothetical protein
RA 1,619,115 T→G 13.6% E260D (GAA→GAC)  nadB ← L‑aspartate oxidase
RA 1,630,146 G→A 11.4% E180E (GAG→GAA)  pdxJ → Pyridoxine 5'‑phosphate synthase
RA 1,630,540 A→C 36.8% L419R (CTG→CGG)  czcS ← Sensor protein CzcS
RA 1,636,594 T→C 7.6% K402E (AAG→GAG)  lon_1 ← Lon protease
RA 1,718,463 T→G 26.5% Q65P (CAG→CCG)  CJ019_01614 ← hypothetical protein
RA 1,832,343 C→T 6.9% D78N (GAC→AAC)  yfgD ← putative protein YfgD
RA 1,892,414 A→C 26.7% intergenic (+428/‑92) PP_RS08755 → / → napA tRNA‑Asp/Periplasmic nitrate reductase
RA 1,930,927 A→G 9.8% F396L (TTC→CTC)  CJ019_01847 ← hypothetical protein
RA 2,094,817 T→G 60.0% Q183P (CAG→CCG)  CJ019_01995 ← hypothetical protein
RA 2,391,010 T→G 48.9% E566D (GAA→GAC)  bvgS ← Virulence sensor protein BvgS
RA 2,487,466 C→T 8.5% D77N (GAC→AAC)  uspE_1 ← Universal stress protein E
RA 2,503,428 C→T 7.3% G454S (GGT→AGT)  copA_2 ← Copper resistance protein A
RA 2,517,936 C→T 8.5% P521L (CCG→CTG)  acsA_1 → Acetyl‑coenzyme A synthetase
RA 2,708,478 T→G 32.0% C46G (TGC→GGC)  CJ019_02558 → hypothetical protein
RA 2,745,758 A→T 6.9% A86A (GCA→GCT)  czcB_2 → Cobalt‑zinc‑cadmium resistance protein CzcB
RA 2,759,782 G→A 7.8% A645A (GCC→GCT)  cntO_2 ← Metal‑pseudopaline receptor CntO
RA 2,812,541 A→T 6.9% D85V (GAC→GTC)  CJ019_02665 → hypothetical protein
RA 2,958,255 G→T 7.3% Q477K (CAG→AAG)  irtB ← Iron import ATP‑binding/permease protein IrtB
RA 3,047,252 T→G 13.7% S111R (AGC→CGC)  CJ019_02862 ← hypothetical protein
RA 3,065,508 G→A 100% V53M (GTG→ATG)  rcsC_6 → Sensor histidine kinase RcsC
RA 3,117,533 A→T 6.1% G259G (GGT→GGA)  CJ019_02936 ← hypothetical protein
RA 3,139,338 T→G 13.5% L235R (CTG→CGG)  lsrD → Autoinducer 2 import system permease proteinLsrD
RA 3,146,945 T→A 7.8% F31Y (TTC→TAC)  CJ019_02964 → hypothetical protein
RA 3,302,084 G→A 9.8% G48S (GGC→AGC)  lhgD → L‑2‑hydroxyglutarate dehydrogenase
RA 3,308,718 A→C 29.7% R166R (CGT→CGG)  CJ019_03110 ← hypothetical protein
RA 3,427,284 G→A 7.7% V127I (GTC→ATC)  CJ019_03250 → hypothetical protein
RA 3,616,780 G→A 8.5% G110G (GGC→GGT)  hutI_1 ← Imidazolonepropionase
RA 3,671,624 C→A 14.3% intergenic (+1/+42) CJ019_03482 → / ← CJ019_03483 hypothetical protein/hypothetical protein
RA 3,728,717 A→G 8.7% Q186R (CAG→CGG)  cnrA → Nickel and cobalt resistance protein CnrA
RA 3,761,329 A→C 42.6% E96A (GAG→GCG)  CJ019_03574 → hypothetical protein
RA 3,841,593 G→A 7.5% P346P (CCG→CCA)  CJ019_03638 → hypothetical protein
RA 3,895,319 C→T 9.5% R118C (CGC→TGC)  CJ019_03685 → putative protein
RA 3,942,694 A→G 8.5% L162P (CTG→CCG)  surA_2 ← Chaperone SurA
RA 3,957,240 C→T 100% G137R (GGG→AGG)  dmlR_13 ← HTH‑type transcriptional regulator DmlR
RA 3,986,622 T→G 38.9% D31A (GAT→GCT)  CJ019_03763 ← hypothetical protein
RA 4,097,408 C→A 7.3% S101Y (TCC→TAC)  cntO_6 → Metal‑pseudopaline receptor CntO
JC 4,257,351 +CGCGGCCG 100% intergenic (‑280/+8) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,357,973 A→T 8.2% intergenic (+50/+76) CJ019_04103 → / ← CJ019_04104 hypothetical protein/hypothetical protein
RA 4,630,224 C→G 10.8% R442G (CGA→GGA)  pitA_2 → Low‑affinity inorganic phosphate transporter 1
RA 4,685,094 A→C 19.4% Q451H (CAA→CAC)  argD_4 → Acetylornithine/succinyldiaminopimelateaminotrans ferase
RA 4,760,742 A→C 32.8% H41P (CAC→CCC)  vanB → vanillate O‑demethylase oxidoreductase
RA 4,834,069 A→G 7.0% H157R (CAC→CGC)  ccoN1_2 → Cbb3‑type cytochrome c oxidase subunit CcoN1
RA 4,863,130 C→T 9.0% N305N (AAC→AAT)  pucD → putative xanthine dehydrogenase subunit D
RA 4,868,981 T→C 9.5% G68G (GGT→GGC)  adeP_1 → Adenine permease AdeP
RA 4,874,709 A→C 41.5% intergenic (+13/‑174) CJ019_04568 → / → uacT_1 hypothetical protein/Uric acid transporter UacT
RA 5,002,486 T→C 8.1% M1T (ATG→ACG) † CJ019_04695 → hypothetical protein
RA 5,128,518 C→T 10.2% T130T (ACG→ACA)  CJ019_04823 ← hypothetical protein
RA 5,160,922 C→T 6.4% R309H (CGT→CAT)  CJ019_04854 ← hypothetical protein
RA 5,324,255 G→A 8.0% H34H (CAC→CAT)  sfsA ← Sugar fermentation stimulation protein A
RA 5,426,415 A→T 7.7% L499* (TTG→TAG)  hrpB ← ATP‑dependent RNA helicase HrpB
RA 5,468,407 G→A 6.3% G221R (GGA→AGA)  CJ019_05146 → Putative 3‑methyladenine DNA glycosylase
RA 5,508,974 C→G 18.0% F46L (TTC→TTG)  dnaK_2 → Chaperone protein DnaK
RA 5,688,615 T→G 56.2% R228R (CGT→CGG)  pyrC' → Dihydroorotase‑like protein
RA 5,688,637 A→C 58.0% S236R (AGC→CGC)  pyrC' → Dihydroorotase‑like protein
RA 5,688,645 T→G 46.6% R238R (CGT→CGG)  pyrC' → Dihydroorotase‑like protein
RA 5,756,055 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 5,806,024 G→T 13.8% A97S (GCC→TCC)  argS → Arginine‑‑tRNA ligase
RA 5,881,004 G→A 9.6% M1I (ATG→ATA) † quiP → Acyl‑homoserine lactone acylase QuiP
RA 6,084,764 A→C 29.1% N178T (AAC→ACC)  paiB → Protease synthase and sporulation protein PAI 2
RA 6,119,958 G→C 18.8% L195V (CTT→GTT)  gcvA_13 ← Glycine cleavage system transcriptionalactivator
RA 6,182,018 C→T 7.7% S222N (AGC→AAC)  yidC ← Membrane protein insertase YidC

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB122 87997 88060 64 12 [11] [10] 15 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB122 161232 161419–161317 86–188 12 [11] [11] 12 [uctC_1] [uctC_1]
* * ÷ ACB122 277604 277677 74 16 [11] [9] 12 [tauD_2] [tauD_2]
* * ÷ ACB122 309026 309109 84 12 [11] [10] 13 [cysQ] [cysQ]
* * ÷ ACB122 329220 329352 133 13 [11] [9] 17 [CJ019_00302] [CJ019_00302]
* * ÷ ACB122 346106 346210 105 13 [11] [11] 13 [btuD_1] [btuD_1]
* * ÷ ACB122 517195 517311 117 15 [6] [11] 12 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB122 607283 607400 118 13 [11] [11] 18 dxs/ispA 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/Farnesyl diphosphate synthase
* * ÷ ACB122 641270 641348 79 12 [11] [11] 12 [acoR_2] [acoR_2]
* * ÷ ACB122 661108 661213 106 12 [11] [11] 12 yfhM/CJ019_00619 Alpha‑2‑macroglobulin/hypothetical protein
* * ÷ ACB122 674267 674380 114 13 [11] [8] 12 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB122 711474 711584 111 16 [11] [11] 13 [thiO]–[aam] [thiO],[aam]
* * ÷ ACB122 789837 789977 141 12 [11] [11] 12 [CJ019_00751] [CJ019_00751]
* * ÷ ACB122 856909 856981 73 12 [11] [6] 13 [hemH]–[uraA] [hemH],[uraA]
* * ÷ ACB122 876827 876988 162 13 [11] [10] 12 CJ019_00843/malT putative protein/HTH‑type transcriptional regulator MalT
* * ÷ ACB122 948171 948237 67 13 [11] [10] 14 cyoE/alaC Protoheme IX farnesyltransferase/Glutamate‑pyruvate aminotransferase AlaC
* * ÷ ACB122 1000517 1000643 127 14 [10] [11] 12 [fecA_1]–[osmV] [fecA_1],[osmV]
* * ÷ ACB122 1119656 1119709 54 12 [9] [11] 12 tdcG_2/gcvP_1 L‑serine dehydratase TdcG/Glycine dehydrogenase (decarboxylating)
* * ÷ ACB122 1360641 1360963 323 12 [11] [10] 12 CJ019_01275 hypothetical protein
* * ÷ ACB122 1396583 1396663 81 12 [8] [8] 12 [CJ019_01313] [CJ019_01313]
* * ÷ ACB122 1457207 1457284 78 12 [11] [10] 13 [algL]–[algX] [algL],[algX]
* * ÷ ACB122 1492483 1492568 86 13 [11] [11] 12 CJ019_01406/zapE_1 hypothetical protein/Cell division protein ZapE
* * ÷ ACB122 1499914 1500063 150 12 [11] [11] 12 [petC]–[sspA] [petC],[sspA]
* * ÷ ACB122 1537435 1537550 116 13 [11] [4] 15 [mdfA] [mdfA]
* * ÷ ACB122 1585608 1585721 114 14 [11] [11] 12 CJ019_01493 hypothetical protein
* * ÷ ACB122 1632599 1632684 86 12 [10] [11] 18 czcR_4/CJ019_01536 Transcriptional activator protein CzcR/hypothetical protein
* * ÷ ACB122 1697671 1697728 58 12 [11] [11] 16 CJ019_01593/CJ019_01594 hypothetical protein/hypothetical protein
* * ÷ ACB122 1705097 1705203 107 12 [9] [10] 13 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB122 1833103 1833206 104 13 [8] [10] 12 [resA_1]–[CJ019_01751] [resA_1],[CJ019_01751]
* * ÷ ACB122 1835835 1835886 52 13 [11] [10] 12 barA Signal transduction histidine‑protein kinaseBarA
* * ÷ ACB122 1914560 1914667 108 16 [10] [11] 12 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB122 1923425 1923503 79 15 [10] [11] 12 [apeB] [apeB]
* * ÷ ACB122 1940798 1940935 138 12 [9] [10] 13 CJ019_01857/gshAB hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB
* * ÷ ACB122 2031287 2031451 165 12 [10] [11] 12 [wecB] [wecB]
* * ÷ ACB122 2234303 2234410 108 13 [11] [10] 12 [gltX] [gltX]
* * ÷ ACB122 2287031 2287124 94 12 [11] [11] 12 [CJ019_02168]–[CJ019_02169] [CJ019_02168],[CJ019_02169]
* * ÷ ACB122 2288822 2288932 111 12 [11] [11] 14 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ ACB122 2422922 2423000 79 12 [11] [11] 14 [ycbX] [ycbX]
* * ÷ ACB122 2471436 2471561 126 13 [10] [10] 13 [CJ019_02330] [CJ019_02330]
* * ÷ ACB122 2646613 2646716 104 12 [11] [11] 12 [CJ019_02505] [CJ019_02505]
* * ÷ ACB122 3046158 3046321 164 12 [11] [11] 12 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB122 3069112 3069195 84 14 [10] [11] 14 [CJ019_02882] [CJ019_02882]
* * ÷ ACB122 3145279 3145423 145 12 [11] [11] 12 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ ACB122 3305722 3305811 90 12 [10] [11] 13 CJ019_03107/hemB_1 hypothetical protein/Delta‑aminolevulinic acid dehydratase
* * ÷ ACB122 3459838 3459932 95 12 [11] [10] 12 CJ019_03284 hypothetical protein
* * ÷ ACB122 3769404 3769474 71 13 [11] [11] 12 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB122 3839303 3839412 110 13 [11] [10] 12 [argP_2] [argP_2]
* * ÷ ACB122 3944689 3944853 165 12 [10] [11] 12 CJ019_03729/CJ019_03730 hypothetical protein/hypothetical protein
* * ÷ ACB122 4163777 4163873 97 12 [8] [9] 13 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB122 4344771 4344882 112 12 [10] [11] 13 nmoA Nitronate monooxygenase
* * ÷ ACB122 4495354 4495446 93 16 [11] [11] 13 [xanP]–[dsrE] [xanP],[dsrE]
* * ÷ ACB122 4521607 4521669 63 14 [10] [9] 13 [CJ019_04289] [CJ019_04289]
* * ÷ ACB122 4543576 4543704 129 13 [7] [11] 12 [rutR_2] [rutR_2]
* * ÷ ACB122 4666845 4666999 155 12 [11] [9] 12 [btuB_4] [btuB_4]
* * ÷ ACB122 4732421 4732488 68 13 [8] [11] 12 gltA/CJ019_04468 Citrate synthase/hypothetical protein
* * ÷ ACB122 4773158 4773259 102 12 [11] [11] 12 [lgrB_1] [lgrB_1]
* * ÷ ACB122 4836801 4836909 109 15 [9] [10] 12 [ccoP2_2] [ccoP2_2]
* * ÷ ACB122 4944867 4944981 115 13 [11] [8] 12 [CJ019_04642] [CJ019_04642]
* * ÷ ACB122 5156446 5156578 133 14 [8] [11] 12 CJ019_04852/CJ019_04853 hypothetical protein/Beta‑ketodecanoyl‑[acyl‑carrier‑protein]synthase
* * ÷ ACB122 5167214 5167232 19 12 [0] [10] 23 fadD_1/fadD_2 Long‑chain‑fatty‑acid‑‑CoA ligase/Long‑chain‑fatty‑acid‑‑CoA ligase
* * ÷ ACB122 5193582 5193667 86 13 [11] [11] 12 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB122 5204207 5204253 47 13 [10] [11] 12 rnd/eptA_2 Ribonuclease D/Phosphoethanolamine transferase EptA
* * ÷ ACB122 5331982 5332078 97 14 [8] [11] 14 zraR/pcnB Transcriptional regulatory protein ZraR/Poly(A) polymerase I
* * ÷ ACB122 5499114 5499280 167 13 [11] [11] 12 [CJ019_05176] [CJ019_05176]
* * ÷ ACB122 5529658 5529757 100 13 [11] [11] 14 [nadE] [nadE]
* * ÷ ACB122 5550459 5550585 127 12 [11] [10] 16 CJ019_05227/purA hypothetical protein/Adenylosuccinate synthetase
* * ÷ ACB122 5664259 5664374 116 13 [10] [8] 12 CJ019_05320/CJ019_05321 hypothetical protein/hypothetical protein
* * ÷ ACB122 5674050 5674123 74 12 [11] [11] 13 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB122 5726655 5726768 114 13 [11] [11] 13 proY_2/hutH Proline‑specific permease ProY/Histidine ammonia‑lyase
* * ÷ ACB122 5809543 5809645 103 12 [4] [11] 12 [pilT] [pilT]
* * ÷ ACB122 5895764 5895854 91 12 [11] [10] 12 [CJ019_05521] [CJ019_05521]
* * ÷ ACB122 6073610 6073691 82 12 [11] [11] 12 [CJ019_05690] [CJ019_05690]