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 55,609 C→T 5.9% G76G (GGC→GGT)  alkJ_1 → Alcohol dehydrogenase [acceptor]
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 194,448 G→A 7.5% D3103N (GAC→AAC)  CJ019_00185 → hypothetical protein
RA 504,981 T→A 25.4% intergenic (+71/‑77) trpC → / → CJ019_00453 Indole‑3‑glycerol phosphate synthase/hypothetical protein
RA 627,228 T→G 33.9% S162A (TCG→GCG)  acoR_1 → Acetoin catabolism regulatory protein
RA 627,234 A→C 27.4% S164R (AGC→CGC)  acoR_1 → Acetoin catabolism regulatory protein
RA 843,700 A→T 7.6% intergenic (‑233/‑572) CJ019_00805 ← / → hemA hypothetical protein/Glutamyl‑tRNA reductase
RA 881,214 C→T 6.9% Q400* (CAG→TAG)  lapB → Lipopolysaccharide assembly protein B
RA 1,026,049 T→A 6.0% L346M (TTG→ATG)  nylB → 6‑aminohexanoate‑dimer hydrolase
RA 1,114,332 C→T 8.7% P241S (CCC→TCC)  lptF → Lipopolysaccharide export system permeaseprotein LptF
RA 1,312,115 C→T 25.7% Q96* (CAA→TAA)  aaeA_2 → p‑hydroxybenzoic acid efflux pump subunit AaeA
RA 1,396,806 T→A 9.1% E643D (GAA→GAT)  mcpU_1 ← Methyl‑accepting chemotaxis protein McpU
RA 1,513,121 C→A 7.8% F135L (TTC→TTA)  mraY → Phospho‑N‑acetylmuramoyl‑pentapeptide‑transferas e
RA 1,639,779 T→G 28.5% N212H (AAC→CAC)  gcd ← Quinoprotein glucose dehydrogenase
RA 1,943,813 C→T 9.7% L230L (CTG→CTA)  asnB ← Asparagine synthetase [glutamine‑hydrolyzing] 1
RA 2,074,834 T→A 8.0% K149* (AAA→TAA)  ohrR ← Organic hydroperoxide resistance transcriptional regulator
RA 2,094,808 A→C 41.3% L186R (CTG→CGG)  CJ019_01995 ← hypothetical protein
RA 2,094,817 T→G 44.9% Q183P (CAG→CCG)  CJ019_01995 ← hypothetical protein
JC 2,191,046 +CTGAAAATATCTCTTAT 100% intergenic (‑1/‑313) PP_RS10045 ← / → purU_3 LysR family transcriptional regulator/Formyltetrahydrofolate deformylase
RA 2,493,436 T→C 5.8% F760S (TTC→TCC)  iutA → Ferric aerobactin receptor
RA 2,630,169 A→G 8.7% D31G (GAC→GGC)  CJ019_02487 → hypothetical protein
RA 2,800,374 C→T 8.9% I247I (ATC→ATT)  rihA → Pyrimidine‑specific ribonucleoside hydrolaseRihA
RA 3,257,672 T→C 11.4% intergenic (‑86/‑215) mcpP ← / → uppP Methyl‑accepting chemotaxis protein McpP/Undecaprenyl‑diphosphatase
RA 3,294,290 T→C 8.2% I52V (ATC→GTC)  CJ019_03098 ← Peptidyl‑prolyl cis‑trans isomerase cyp18
RA 3,317,589 C→T 8.1% G185G (GGG→GGA)  CJ019_03118 ← hypothetical protein
RA 3,440,331 T→G 44.5% A19A (GCT→GCG)  CJ019_03266 → hypothetical protein
RA 3,880,619 C→A 9.3% G271V (GGT→GTT)  rcsC_9 ← Sensor histidine kinase RcsC
RA 4,159,020 T→G 30.6% K237T (AAG→ACG)  proP_4 ← Proline/betaine transporter
RA 4,245,128 A→C 22.8% L178R (CTG→CGG)  CJ019_03982 ← Crotonyl‑CoA hydratase
JC 4,257,334 +CGCGGCCG 100% intergenic (‑280/+8) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,509,674 G→A 9.5% S481S (TCC→TCT)  clpA ← ATP‑dependent Clp protease ATP‑binding subunitClpA
RA 4,557,768 G→A 8.1% A472T (GCC→ACC)  glgA → Glycogen synthase
RA 4,720,069 T→G 9.6% D67A (GAC→GCC) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,070 C→T 8.2% D67N (GAC→AAC) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,077 G→A 8.7% T64T (ACC→ACT)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,080 C→G 8.5% A63A (GCG→GCC)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,083 T→A 7.8% E62D (GAA→GAT) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,084 T→G 7.7% E62A (GAA→GCA) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,086 C→A 8.7% V61V (GTG→GTT)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,095 C→A 8.7% K58N (AAG→AAT) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,096 T→C 8.9% K58R (AAG→AGG) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,097 T→G 8.9% K58Q (AAG→CAG) ‡ sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,098 G→C 9.1% V57V (GTC→GTG)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,122 C→G 8.9% L49L (CTG→CTC)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,137 A→G 8.6% G44G (GGT→GGC)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,140 C→T 8.8% K43K (AAG→AAA)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,143 G→A 8.7% G42G (GGC→GGT)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,720,161 G→A 7.8% V36V (GTC→GTT)  sucD ← Succinate‑‑CoA ligase [ADP‑forming] subunitalpha
RA 4,729,213 G→C 10.8% A252A (GCC→GCG)  sdhA_2 ← Succinate dehydrogenase flavoprotein subunit
RA 4,759,509 G→A 100% intergenic (+124/‑16) fpvA_3 → / → ligM_KToptimized Ferripyoverdine receptor/sequence generated by OPTIMIZER for KT2440
RA 4,951,360 C→T 7.4% G219D (GGC→GAC)  fliG ← Flagellar motor switch protein FliG
RA 5,037,507 C→T 5.8% H420Y (CAT→TAT)  CJ019_04731 → hypothetical protein
RA 5,087,838 C→T 5.8% P229P (CCG→CCA)  occM_3 ← Octopine transport system permease protein OccM
RA 5,096,415 C→G 37.1% intergenic (+28/‑162) CJ019_04792 → / → CJ019_04793 Putative pterin‑4‑alpha‑carbinolaminedehydratase/hypothetical protein
RA 5,300,670 T→G 45.8% intergenic (‑100/+3473) recC ← / ← PP_RS08750 RecBCD enzyme subunit RecC/tRNA‑Val
RA 5,345,373 A→T 51.3% L688Q (CTG→CAG)  pnp ← Polyribonucleotide nucleotidyltransferase
RA 5,386,500 C→A 100% intergenic (‑509/+1142) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,503 C→G 100% intergenic (‑512/+1139) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,506 1 bp→GT 100% intergenic (‑515/+1136) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,507:1 +C 100% intergenic (‑516/+1135) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,510 2 bp→TA 100% intergenic (‑519/+1131) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,512:1 +AA 100% intergenic (‑521/+1130) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,514 T→C 100% intergenic (‑523/+1128) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,517 G→C 100% intergenic (‑526/+1125) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,519 G→A 100% intergenic (‑528/+1123) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
RA 5,386,811 C→T 100% intergenic (‑820/+831) CJ019_05070 ← / ← nptII hypothetical protein/neomycin phosphotransferase
JC 5,389,996 Δ8 bp 100% coding (90‑97/1666 nt) ligH → 10‑formyltetrahydrofolate synthetase
RA 5,481,135 A→G 8.9% D155G (GAC→GGC)  purH → Bifunctional purine biosynthesis protein PurH
RA 5,507,093 T→G 54.5% L36R (CTC→CGC)  CJ019_05179 → hypothetical protein
RA 5,693,153 T→G 33.6% R228R (CGT→CGG)  pyrC' → Dihydroorotase‑like protein
RA 5,693,175 A→C 54.2% S236R (AGC→CGC)  pyrC' → Dihydroorotase‑like protein
RA 5,693,183 T→G 42.5% R238R (CGT→CGG)  pyrC' → Dihydroorotase‑like protein
RA 5,760,593 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 6,089,343 A→C 18.5% S192R (AGC→CGC)  paiB → Protease synthase and sporulation protein PAI 2
RA 6,129,757 A→T 31.0% H430Q (CAT→CAA)  copA_4 ← Copper resistance protein A

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB143 87969 88046 78 14 [12] [12] 14 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB143 161217 161438–161317 101–222 14 [12] [11] 13 [uctC_1] [uctC_1]
* * ÷ ACB143 517198 517278 81 14 [5] [12] 13 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB143 661102 661215 114 13 [7] [12] 13 yfhM/CJ019_00619 Alpha‑2‑macroglobulin/hypothetical protein
* * ÷ ACB143 674272 674396 125 14 [12] [12] 13 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB143 711464 711566 103 14 [11] [11] 15 [thiO]–[aam] [thiO],[aam]
* * ÷ ACB143 1376260 1376336 77 13 [12] [12] 17 CJ019_01289 hypothetical protein
* * ÷ ACB143 1396596 1396672 77 13 [12] [11] 14 [mcpU_1] [mcpU_1]
* * ÷ ACB143 1457225 1457310 86 15 [10] [12] 13 [algX] [algX]
* * ÷ ACB143 1608717 1608797 81 14 [12] [11] 13 CJ019_01513 hypothetical protein
* * ÷ ACB143 1696210 1696359 150 13 [12] [11] 13 lysS/CJ019_01592 Lysine‑‑tRNA ligase/hypothetical protein
* * ÷ ACB143 1697655 1697720 66 13 [12] [12] 13 [CJ019_01593] [CJ019_01593]
* * ÷ ACB143 1923378 1923505 128 13 [12] [10] 14 [apeB] [apeB]
* * ÷ ACB143 1940792 1940944 153 15 [12] [11] 14 [CJ019_01857] [CJ019_01857]
* * ÷ ACB143 2092961 2093072 112 14 [11] [12] 15 rcsC_3/CJ019_01993 Sensor histidine kinase RcsC/hypothetical protein
* * ÷ ACB143 2288844 2288921 78 13 [12] [10] 13 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ ACB143 3046191 3046330 140 14 [12] [11] 15 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB143 3581125 3581203 79 13 [9] [12] 14 [ydcO_3] [ydcO_3]
* * ÷ ACB143 3769381 3769475 95 13 [12] [12] 13 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB143 4163780 4163856 77 14 [10] [9] 13 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB143 4344734 4344818 85 13 [12] [12] 14 nmoA Nitronate monooxygenase
* * ÷ ACB143 4521580 4521661 82 14 [10] [12] 13 [CJ019_04289] [CJ019_04289]
* * ÷ ACB143 4732414 4732479 66 15 [11] [12] 13 [CJ019_04468] [CJ019_04468]
* * ÷ ACB143 4845710 4845850 141 17 [11] [12] 17 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB143 4944229 4944345 117 13 [12] [11] 13 [CJ019_04642] [CJ019_04642]
* * ÷ ACB143 5192923 5193039 117 14 [12] [12] 13 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB143 5503654 5503811 158 13 [12] [12] 13 [CJ019_05176] [CJ019_05176]
* * ÷ ACB143 5534204 5534320 117 13 [12] [12] 13 [nadE]–[CJ019_05208] [nadE],[CJ019_05208]
* * ÷ ACB143 5650148 5650237 90 14 [12] [12] 14 CJ019_05302/CJ019_05303 hypothetical protein/hypothetical protein
* * ÷ ACB143 5678573 5678659 87 13 [12] [11] 13 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB143 5737640 5737695 56 14 [12] [12] 13 CJ019_05378/blc_2 8‑oxoguanine deaminase/Outer membrane lipoprotein Blc
* * ÷ ACB143 5814049 5814187 139 13 [12] [12] 13 [pilT] [pilT]
* * ÷ ACB143 5894912 5895006 95 14 [12] [10] 13 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ ACB143 5900331 5900394 64 15 [11] [12] 13 [CJ019_05521] [CJ019_05521]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB143 737971 =NA (NA)20 (0.450) 12/242 NT 95.2% coding (13/276 nt) CJ019_00701 hypothetical protein
?ACB143 1812806 = 1 (0.020)coding (995/1008 nt) rpoS RNA polymerase sigma factor RpoS
* ? ACB143 = 18128131 (0.020)32 (0.730) 24/242 NT 97.0% coding (1002/1008 nt) rpoS RNA polymerase sigma factor RpoS
?ACB143 4527800 = NA (NA)intergenic (+730/‑85) CJ019_04293/CJ019_00703 hypothetical protein/hypothetical protein
* ? ACB143 3359593 =44 (1.000)11 (0.250) 9/240 NT 26.0% intergenic (+219/‑151) pikAII_1/CJ019_03160 Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42
?ACB143 5345402 = 19 (0.430)coding (2034/2106 nt) pnp Polyribonucleotide nucleotidyltransferase
* ? ACB143 = 337660539 (0.890)13 (0.300) 12/242 NT 31.3% coding (501/546 nt) CJ019_03184 hypothetical protein
?ACB143 = 5345406 18 (0.410)coding (2030/2106 nt) pnp Polyribonucleotide nucleotidyltransferase