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 10,913 G→A 10.0% W95* (TGG→TAG)  CJ019_00019 → hypothetical protein
RA 44,293 Δ1 bp 100% intergenic (+124/‑367) oprD_1 → / → czcR_2 Porin D/Transcriptional activator protein CzcR
RA 96,480 T→G 47.3% intergenic (+121/‑72) cynT → / → CJ019_00104 Carbonic anhydrase 1/hypothetical protein
RA 120,975 Δ1 bp 100% intergenic (+272/+100) polA → / ← engB DNA polymerase I/putative GTP‑binding protein EngB
RA 150,804 A→C 48.2% W7G (TGG→GGG)  CJ019_00156 ← hypothetical protein
RA 169,760 A→C 11.6% intergenic (+724/+2963) PP_RS08750 → / ← fhuA_1 tRNA‑Val/Ferrichrome outer membrane transporter/phagereceptor
RA 172,649 C→T 8.2% intergenic (+3613/+74) PP_RS08750 → / ← fhuA_1 tRNA‑Val/Ferrichrome outer membrane transporter/phagereceptor
RA 179,484 T→C 100% C316R (TGC→CGC)  CJ019_00182 → hypothetical protein
RA 523,499 G→T 13.9% W121C (TGG→TGT)  birA → Bifunctional ligase/repressor BirA
RA 627,220 T→G 55.7% L159R (CTG→CGG)  acoR_1 → Acetoin catabolism regulatory protein
RA 627,228 T→G 48.8% S162A (TCG→GCG)  acoR_1 → Acetoin catabolism regulatory protein
RA 956,989 C→T 13.8% P183L (CCG→CTG)  metN_3 → Methionine import ATP‑binding protein MetN
RA 1,052,536 T→G 30.8% S90R (AGC→CGC)  argO ← Arginine exporter protein ArgO
RA 1,066,951 C→T 9.7% S319S (TCG→TCA)  gatA ← Glutamyl‑tRNA(Gln) amidotransferase subunit A
RA 1,299,176 A→G 8.7% I65T (ATC→ACC)  livH_2 ← High‑affinity branched‑chain amino acidtransport system permease protein LivH
RA 1,375,132 C→G 9.3% A277G (GCC→GGC)  dinB → DNA polymerase IV
RA 1,497,924 C→T 13.3% G191G (GGC→GGT)  petA → Ubiquinol‑cytochrome c reductase iron‑sulfursubunit
RA 1,718,463 T→G 34.8% Q65P (CAG→CCG)  CJ019_01614 ← hypothetical protein
RA 1,719,504 G→A 9.5% P572P (CCC→CCT)  plsB ← Glycerol‑3‑phosphate acyltransferase
RA 1,806,734 C→A 100% S11R (AGC→AGA)  yeiG → S‑formylglutathione hydrolase YeiG
RA 1,903,353 C→T 10.2% G172D (GGT→GAT)  dgoT_1 ← D‑galactonate transporter
RA 1,919,925 A→G 9.5% intergenic (‑4/‑324) CJ019_01835 ← / → phnR hypothetical protein/Putative transcriptional regulator of 2‑aminoethylphosphonate degradation operons
RA 1,920,126 C→T 11.1% intergenic (‑205/‑123) CJ019_01835 ← / → phnR hypothetical protein/Putative transcriptional regulator of 2‑aminoethylphosphonate degradation operons
RA 1,973,043 A→G 14.8% N201S (AAC→AGC)  rpsA → 30S ribosomal protein S1
RA 2,006,436 G→A 8.5% P175S (CCT→TCT)  CJ019_01905 ← hypothetical protein
RA 2,384,716 G→T 11.9% S63I (AGC→ATC)  CJ019_02252 → hypothetical protein
RA 2,385,345 T→G 35.6% L273V (TTG→GTG)  CJ019_02252 → hypothetical protein
RA 2,527,924 G→A 7.3% R306C (CGC→TGC)  mrpD_2 ← Na( )/H( ) antiporter subunit D
RA 3,033,280 G→T 9.9% V436V (GTG→GTT)  lgoT_1 → putative L‑galactonate transporter
RA 3,065,799 T→G 73.7% F150V (TTT→GTT)  rcsC_6 → Sensor histidine kinase RcsC
RA 3,143,328 G→C 18.2% A125A (GCG→GCC)  CJ019_02960 → hypothetical protein
RA 3,886,771 T→C 8.7% F164L (TTC→CTC)  rarD_2 → Protein RarD
RA 4,029,463 A→C 31.3% D290A (GAC→GCC)  mcpU_3 → Methyl‑accepting chemotaxis protein McpU
RA 4,135,607 A→C 51.5% Q32P (CAG→CCG)  tgnC → (Z)‑2‑((N‑methylformamido)methylene)‑5‑hydroxybu tyrolactone dehydrogenase
RA 4,214,479 A→G 13.0% K384R (AAG→AGG)  CJ019_03954 → hypothetical protein
JC 4,257,351 +CGCGGCCG 100% intergenic (‑280/+8) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,266,097 A→C 100% D147A (GAC→GCC)  CJ019_04001 → putative FAD‑linked oxidoreductase
RA 4,469,342 C→T 10.5% A88A (GCG→GCA)  sasA_16 ← Adaptive‑response sensory‑kinase SasA
RA 4,487,862 C→A 9.6% V186V (GTC→GTA)  CJ019_04257 → hypothetical protein
RA 4,593,393 C→T 11.4% A39T (GCG→ACG)  CJ019_04342 ← hypothetical protein
RA 4,759,486 A→G 15.4% intergenic (+84/‑55) fpvA_3 → / → vanA Ferripyoverdine receptor/vanillate demethylase A
RA 4,759,487 A→T 15.4% intergenic (+85/‑54) fpvA_3 → / → vanA Ferripyoverdine receptor/vanillate demethylase A
RA 4,801,948 G→T 38.9% intergenic (‑268/‑463) CJ019_04509 ← / → dsbD_2 hypothetical protein/Thiol:disulfide interchange protein DsbD
RA 4,912,296 A→T 15.6% S244C (AGC→TGC)  CJ019_04608 → hypothetical protein
RA 4,950,614 G→A 10.8% R30C (CGC→TGC)  fliI ← Flagellum‑specific ATP synthase
MC JC 4,963,801 Δ8,879 bp 100% [CJ019_04659]–[flgG] [CJ019_04659], fabH, CJ019_04661, CJ019_04662, CJ019_04663, flgI, flgH, [flgG]
RA 5,094,168 A→C 28.7% F476C (TTT→TGT)  tyrR_2 ← Transcriptional regulatory protein TyrR
RA 5,094,419 A→G 12.1% H392H (CAT→CAC)  tyrR_2 ← Transcriptional regulatory protein TyrR
RA 5,401,606 C→T 8.9% P639P (CCG→CCA)  stcD_2 ← putative N‑methylproline demethylase
RA 5,544,167 A→G 12.5% E250G (GAA→GGA)  CJ019_05222 → hypothetical protein
RA 5,622,704 Δ1 bp 7.4% coding (212/1629 nt) putP ← Sodium/proline symporter
RA 5,644,969 C→A 8.4% A51S (GCC→TCC)  cbbA ← Fructose‑bisphosphate aldolase
RA 5,756,055 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 6,095,820 A→T 15.9% intergenic (+129/‑4) uvrD_2 → / → CJ019_05710 DNA helicase II/hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB122 80685 80839 155 7 [6] [4] 8 [gcvA_2] [gcvA_2]
* * ÷ ACB122 87979 88050 72 7 [6] [6] 7 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB122 213580 213659 80 7 [6] [5] 7 [CJ019_00185] [CJ019_00185]
* * ÷ ACB122 277577 277660 84 9 [6] [4] 7 [betT2] [betT2]
* * ÷ ACB122 329263 329350 88 7 [4] [6] 7 CJ019_00302/CJ019_00303 hypothetical protein/hypothetical protein
* * ÷ ACB122 346125 346242 118 7 [6] [6] 7 [btuD_1] [btuD_1]
* * ÷ ACB122 517193 517343 151 7 [3] [6] 9 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB122 641244 641321 78 7 [6] [6] 8 [acoR_2] [acoR_2]
* * ÷ ACB122 674248 674380 133 8 [6] [3] 7 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB122 690141 690203 63 7 [6] [6] 7 bauC/PP_RS08750 Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val
* * ÷ ACB122 711492 711556 65 8 [6] [5] 8 thiO/aam Glycine oxidase/Acylamidase
* * ÷ ACB122 789837 789950 114 9 [6] [6] 7 [CJ019_00751] [CJ019_00751]
* * ÷ ACB122 856933 857026 94 7 [6] [6] 7 [hemH]–[uraA] [hemH],[uraA]
* * ÷ ACB122 860928 861071 144 7 [6] [5] 7 [CJ019_00824] [CJ019_00824]
* * ÷ ACB122 908096 908207 112 9 [6] [6] 10 fruA/CJ019_00870 PTS system fructose‑specific EIIB'BC component/hypothetical protein
* * ÷ ACB122 1000514 1000615 102 7 [6] [5] 7 [fecA_1] [fecA_1]
* * ÷ ACB122 1006232 1006383 152 7 [6] [6] 7 [spuD_1] [spuD_1]
* * ÷ ACB122 1117566 1117623 58 7 [6] [6] 7 gcvT_1 Aminomethyltransferase
* * ÷ ACB122 1141838 1141864 27 8 [6] [5] 8 CJ019_01079 hypothetical protein
* * ÷ ACB122 1304780 1304848 69 7 [5] [6] 8 CJ019_01223/rapA putative signaling protein/RNA polymerase‑associated protein RapA
* * ÷ ACB122 1360633 1360914 282 10 [6] [5] 7 CJ019_01275 hypothetical protein
* * ÷ ACB122 1376293 1376321 29 16 [5] [4] 7 CJ019_01289 hypothetical protein
* * ÷ ACB122 1396600 1396677 78 7 [5] [5] 7 [mcpU_1] [mcpU_1]
* * ÷ ACB122 1457207 1457282 76 8 [6] [6] 9 [algL]–[algX] [algL],[algX]
* * ÷ ACB122 1480077 1480255 179 9 [5] [6] 7 [degS] [degS]
* * ÷ ACB122 1499954 1500039 86 7 [6] [6] 7 petC/sspA Ammonia monooxygenase gamma subunit/Stringent starvation protein A
* * ÷ ACB122 1585623 1585683 61 7 [6] [6] 7 CJ019_01493 hypothetical protein
* * ÷ ACB122 1632607 1632684 78 7 [6] [5] 10 czcR_4/CJ019_01536 Transcriptional activator protein CzcR/hypothetical protein
* * ÷ ACB122 1705087 1705172 86 7 [6] [6] 8 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB122 1835820 1835886 67 7 [6] [5] 7 barA Signal transduction histidine‑protein kinaseBarA
* * ÷ ACB122 1914560 1914664 105 10 [5] [5] 7 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB122 1923425 1923540 116 8 [5] [6] 7 [apeB] [apeB]
* * ÷ ACB122 1940794 1940942 149 7 [6] [6] 7 [CJ019_01857] [CJ019_01857]
* * ÷ ACB122 2043581 2043727 147 7 [6] [4] 7 smrA/CJ019_01939 putative DNA endonuclease SmrA/hypothetical protein
* * ÷ ACB122 2050829 2050897 69 7 [6] [6] 7 [mtnD] [mtnD]
* * ÷ ACB122 2234329 2234381 53 7 [6] [6] 7 gltX/PP_RS08750 Glutamate‑‑tRNA ligase/tRNA‑Val
* * ÷ ACB122 2287048 2287121 74 7 [6] [4] 7 [CJ019_02168]–[CJ019_02169] [CJ019_02168],[CJ019_02169]
* * ÷ ACB122 2288854 2288934 81 7 [6] [6] 7 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ ACB122 2294508 2294629 122 7 [3] [6] 7 sbcD/CJ019_02175 Nuclease SbcCD subunit D/hypothetical protein
* * ÷ ACB122 2830133 2830221 89 7 [6] [6] 7 gabD1/namA_3 Succinate‑semialdehyde dehydrogenase [NADP( )]1/NADPH dehydrogenase
* * ÷ ACB122 3002603 3002679 77 9 [6] [5] 8 [PP_RS08755]–[PP_RS08765] [PP_RS08755],[PP_RS08765]
* * ÷ ACB122 3040199 3040310 112 8 [6] [5] 7 [pstB3]–[CJ019_02856] [pstB3],[CJ019_02856]
* * ÷ ACB122 3046223 3046324 102 7 [6] [5] 7 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB122 3047759 3047865 107 8 [6] [6] 7 CJ019_02862/CJ019_02863 hypothetical protein/hypothetical protein
* * ÷ ACB122 3069100 3069189 90 7 [6] [6] 7 [CJ019_02881]–[CJ019_02882] [CJ019_02881],[CJ019_02882]
* * ÷ ACB122 3145291 3145384 94 7 [6] [6] 8 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ ACB122 3305711 3305805 95 11 [5] [5] 7 [CJ019_03107] [CJ019_03107]
* * ÷ ACB122 3316636 3316693 58 7 [5] [6] 7 CJ019_03117 hypothetical protein
* * ÷ ACB122 3769404 3769471 68 7 [5] [6] 10 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB122 3944703 3944820 118 7 [6] [6] 7 CJ019_03729/CJ019_03730 hypothetical protein/hypothetical protein
* * ÷ ACB122 4043539 4043571 33 8 [6] [6] 7 quiA/oprB_3 Quinate/shikimate dehydrogenase (quinone)/Porin B
* * ÷ ACB122 4163797 4163903 107 7 [5] [6] 7 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB122 4330051 4330154 104 7 [5] [6] 8 [CJ019_04068] [CJ019_04068]
* * ÷ ACB122 4344778 4344823 46 8 [6] [6] 8 nmoA Nitronate monooxygenase
* * ÷ ACB122 4434206 4434261 56 7 [6] [5] 8 nicP_12/nicT_2 Porin‑like protein NicP/Putative metabolite transport protein NicT
* * ÷ ACB122 4521609 4521679 71 7 [6] [6] 11 CJ019_04289/topB Acetyltransferase/DNA topoisomerase 3
* * ÷ ACB122 4543560 4543709 150 7 [6] [6] 7 [rutR_2] [rutR_2]
* * ÷ ACB122 4666896 4666998 103 7 [6] [6] 8 [btuB_4] [btuB_4]
* * ÷ ACB122 4696924 4697101 178 8 [6] [4] 8 [ydiK_3] [ydiK_3]
* * ÷ ACB122 4732426 4732496 71 7 [5] [6] 7 [CJ019_04468] [CJ019_04468]
* * ÷ ACB122 4773154 4773219 66 7 [5] [6] 7 [lgrB_1] [lgrB_1]
* * ÷ ACB122 4802018 4802313 296 10 [6] [6] 8 CJ019_04509/dsbD_2 hypothetical protein/Thiol:disulfide interchange protein DsbD
* * ÷ ACB122 4836834 4836906 73 7 [6] [6] 8 ccoP2_2/CJ019_04535 Cbb3‑type cytochrome c oxidase subunit CcoP2/hypothetical protein
* * ÷ ACB122 4846374 4846501 128 7 [6] [6] 9 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB122 4883503 4883648 146 7 [6] [6] 7 [hyi] [hyi]
* * ÷ ACB122 4890331 4890421 91 7 [6] [6] 9 [CJ019_04582] [CJ019_04582]
* * ÷ ACB122 4944893 4944998 106 7 [6] [6] 7 [CJ019_04642] [CJ019_04642]
* * ÷ ACB122 5156456 5156582 127 7 [4] [4] 7 CJ019_04852/CJ019_04853 hypothetical protein/Beta‑ketodecanoyl‑[acyl‑carrier‑protein]synthase
* * ÷ ACB122 5188804 5188908 105 8 [6] [5] 7 [CJ019_04882]–[pxpC_2] [CJ019_04882],[pxpC_2]
* * ÷ ACB122 5193578 5193691 114 9 [6] [6] 7 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB122 5250796 5250859 64 7 [6] [6] 7 [CJ019_04947] [CJ019_04947]
* * ÷ ACB122 5431907 5431991 85 7 [6] [6] 8 rluE Ribosomal large subunit pseudouridine synthaseE
* * ÷ ACB122 5469772 5469848 77 7 [5] [5] 7 [CJ019_05148] [CJ019_05148]
* * ÷ ACB122 5477764 5477851 88 9 [6] [5] 9 purH/purD Bifunctional purine biosynthesis protein PurH/Phosphoribosylamine‑‑glycine ligase
* * ÷ ACB122 5499111 5499248 138 9 [6] [5] 7 [CJ019_05176] [CJ019_05176]
* * ÷ ACB122 5529684 5529764 81 8 [5] [6] 8 nadE/CJ019_05208 NH(3)‑dependent NAD( ) synthetase/Azurin
* * ÷ ACB122 5531180 5531280 101 8 [6] [5] 8 [CJ019_05210] [CJ019_05210]
* * ÷ ACB122 5550456 5550586 131 7 [6] [5] 7 CJ019_05227/purA hypothetical protein/Adenylosuccinate synthetase
* * ÷ ACB122 5586740 5586818 79 7 [6] [6] 7 CJ019_05260/thiC hypothetical protein/Phosphomethylpyrimidine synthase
* * ÷ ACB122 5645604 5645656 53 7 [6] [3] 8 CJ019_05302/CJ019_05303 hypothetical protein/hypothetical protein
* * ÷ ACB122 5664257 5664369 113 7 [5] [5] 8 CJ019_05320/CJ019_05321 hypothetical protein/hypothetical protein
* * ÷ ACB122 5674006 5674117 112 7 [6] [6] 8 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB122 5752089 5752172 84 7 [6] [6] 8 trmL/secB tRNA (cytidine(34)‑2'‑O)‑methyltransferase/Protein‑export protein SecB
* * ÷ ACB122 5779134 5779217 84 7 [6] [6] 8 selO/trxC Protein adenylyltransferase SelO/Thioredoxin 2
* * ÷ ACB122 5809544 5809649 106 7 [5] [6] 7 [pilT] [pilT]
* * ÷ ACB122 5862957 5862998 42 7 [1] [5] 7 CJ019_05489/ptsP hypothetical protein/Phosphoenolpyruvate‑dependent phosphotransferasesystem
* * ÷ ACB122 5890354 5890445 92 8 [6] [6] 7 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ ACB122 5895785 5895849 65 7 [6] [5] 10 [CJ019_05521] [CJ019_05521]
* * ÷ ACB122 5898089 5898164 76 7 [5] [5] 7 potH Putrescine transport system permease proteinPotH
* * ÷ ACB122 5906755 5906896 142 7 [6] [6] 7 [puuA_5] [puuA_5]
* * ÷ ACB122 5977055 5977116 62 7 [3] [5] 7 [sasA_19] [sasA_19]
* * ÷ ACB122 6073598 6073675 78 8 [6] [6] 7 [yeaD_2]–[CJ019_05690] [yeaD_2],[CJ019_05690]