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 31,613 G→A 5.8% R244Q (CGG→CAG)  oprP → Porin P
RA 44,293 Δ1 bp 100% intergenic (+124/‑367) oprD_1 → / → czcR_2 Porin D/Transcriptional activator protein CzcR
RA 52,849 A→T 6.5% K221* (AAA→TAA)  CJ019_00057 → 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 189,506 T→C 15.7% T1455T (ACT→ACC CJ019_00185 → hypothetical protein
RA 336,468 T→G 26.2% K9N (AAA→AAC CJ019_00309 ← hypothetical protein
RA 382,479 T→G 36.3% L12R (CTG→CGG)  soxD → Sarcosine oxidase subunit delta
RA 399,292 A→C 37.1% intergenic (‑186/+122) CJ019_00365 ← / ← aceF hypothetical protein/Dihydrolipoyllysine‑residue acetyltransferasecomponent of pyruvate dehydrogenase complex
RA 478,896 T→G 30.8% D30A (GAC→GCC)  apaH_1 ← Bis(5'‑nucleosyl)‑tetraphosphatase, symmetrical
RA 486,274 C→A 6.7% P225Q (CCG→CAG)  amgK → N‑acetylmuramate/N‑acetylglucosamine kinase
RA 539,386 G→T 6.7% V55V (GTG→GTT rpsL → 30S ribosomal protein S12
RA 539,395 C→T 6.7% T58T (ACC→ACT rpsL → 30S ribosomal protein S12
RA 539,407 G→A 6.1% E62E (GAG→GAA rpsL → 30S ribosomal protein S12
RA 539,411 T→A 6.2% S64T (TCC→ACC) ‡ rpsL → 30S ribosomal protein S12
RA 539,413 C→T 6.4% S64S (TCC→TCT) ‡ rpsL → 30S ribosomal protein S12
RA 539,416 G→C 6.3% S65S (TCG→TCC rpsL → 30S ribosomal protein S12
RA 539,434 C→T 8.4% G71G (GGC→GGT rpsL → 30S ribosomal protein S12
RA 570,448 A→C 42.2% D599A (GAC→GCC)  fdoG_2 → Formate dehydrogenase‑O major subunit
RA 570,451 T→G 37.4% V600G (GTG→GGG)  fdoG_2 → Formate dehydrogenase‑O major subunit
RA 656,905 A→C 32.8% T241P (ACG→CCG)  yfhM → Alpha‑2‑macroglobulin
RA 797,531 A→C 28.5% intergenic (+77/+17) CJ019_00762 → / ← CJ019_00763 hypothetical protein/hypothetical protein
RA 864,414 C→T 5.3% D24N (GAT→AAT)  CJ019_00828 ← hypothetical protein
RA 930,475 T→G 21.9% T2733P (ACC→CCC)  CJ019_00881 ← hypothetical protein
RA 955,841 T→G 26.6% L84R (CTG→CGG)  phnD1 → putative ABC transporter phosphite bindingprotein PhnD1
RA 1,016,791 A→C 55.4% intergenic (‑53/+26) dppA_1 ← / ← oprD_5 Periplasmic dipeptide transport protein/Porin D
RA 1,021,440 A→T 5.5% F117Y (TTC→TAC)  dppA_3 ← Periplasmic dipeptide transport protein
RA 1,102,967 T→G 6.7% I194S (ATC→AGC)  lutR_2 → HTH‑type transcriptional regulator LutR
RA 1,157,983 A→C 28.9% S162A (TCG→GCG)  hexR_1 ← HTH‑type transcriptional regulator HexR
RA 1,167,947 C→A 6.8% intergenic (+16/‑32) CJ019_01101 → / → CJ019_01102 hypothetical protein/hypothetical protein
RA 1,178,758 T→C 6.7% S304P (TCC→CCC)  purL → Phosphoribosylformylglycinamidine synthase
RA 1,179,510 C→T 87.9% S554S (AGC→AGT purL → Phosphoribosylformylglycinamidine synthase
RA 1,213,098 C→T 8.1% A421T (GCC→ACC)  dctD_2 ← C4‑dicarboxylate transport transcriptionalregulatory protein DctD
RA 1,313,943 A→C 36.0% L614R (CTG→CGG)  CJ019_01235 ← hypothetical protein
RA 1,339,139 T→G 19.7% *269C (TGA→TGC udh ← Uronate dehydrogenase
RA 1,348,419 T→G 22.1% D4A (GAC→GCC)  CJ019_01261 ← hypothetical protein
RA 1,377,714 T→C 6.0% S124G (AGC→GGC)  proS ← Proline‑‑tRNA ligase
RA 1,443,010 T→C 6.0% T17A (ACC→GCC)  prlF ← Antitoxin PrlF
RA 1,523,476 A→C 28.3% D45A (GAC→GCC)  lpxC → UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase
RA 1,523,480 T→G 22.2% P46P (CCT→CCG lpxC → UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase
RA 1,605,593 A→C 23.6% S112R (AGC→CGC)  ung → Uracil‑DNA glycosylase
RA 1,718,463 T→G 29.6% Q65P (CAG→CCG)  CJ019_01614 ← hypothetical protein
RA 1,718,476 T→G 27.1% T61P (ACC→CCC)  CJ019_01614 ← hypothetical protein
RA 1,729,011 T→G 21.1% Q190P (CAG→CCG)  csdA ← Cysteine desulfurase CsdA
RA 1,791,678 T→G 26.5% L182R (CTG→CGG)  lpxB → Lipid‑A‑disaccharide synthase
RA 1,791,684 T→G 24.4% L184R (CTG→CGG)  lpxB → Lipid‑A‑disaccharide synthase
RA 1,806,928 G→T 88.2% G76V (GGG→GTG)  yeiG → S‑formylglutathione hydrolase YeiG
RA 1,837,156 C→A 12.5% G232C (GGC→TGC)  barA ← Signal transduction histidine‑protein kinaseBarA
RA 2,319,429 G→T 7.6% T311K (ACG→AAG)  yjcS ← Putative alkyl/aryl‑sulfatase YjcS
RA 2,413,362 G→A 7.7% A469T (GCG→ACG)  ctpH → Methyl‑accepting chemotaxis protein CtpH
RA 2,491,272 A→C 30.2% H33P (CAC→CCC)  iutA → Ferric aerobactin receptor
RA 2,560,016 T→A 6.1% intergenic (‑53/+90) mcpA ← / ← yhaJ_1 Methyl‑accepting chemotaxis protein McpA/HTH‑type transcriptional regulator YhaJ
RA 2,710,414 A→T 5.3% Y691F (TAC→TTC)  CJ019_02558 → hypothetical protein
RA 2,788,018 T→G 38.1% intergenic (+69/+43) CJ019_02634 → / ← puuB_1 hypothetical protein/Gamma‑glutamylputrescine oxidoreductase
RA 2,847,839 T→A 22.5% N183K (AAT→AAA CJ019_02703 → hypothetical protein
RA 2,947,303 C→T 7.7% M84I (ATG→ATA puuP_2 ← Putrescine importer PuuP
RA 3,047,043 T→A 5.9% A180A (GCA→GCT CJ019_02862 ← hypothetical protein
RA 3,065,799 T→G 67.8% F150V (TTT→GTT)  rcsC_6 → Sensor histidine kinase RcsC
RA 3,119,656 A→C 18.3% F276V (TTC→GTC)  prs2 ← Putative ribose‑phosphate pyrophosphokinase 2
RA 3,228,172 A→G 5.1% G70G (GGA→GGG garD_1 → Galactarate dehydratase (L‑threo‑forming)
RA 3,244,498 A→C 27.7% E94A (GAG→GCG)  ureF → Urease accessory protein UreF
RA 3,267,810 T→G 27.7% L171V (TTG→GTG)  eamA → putative amino‑acid metabolite efflux pump
RA 3,290,008 T→G 21.0% intergenic (‑110/‑42) CJ019_03093 ← / → CJ019_03094 hypothetical protein/hypothetical protein
RA 3,312,455 A→C 28.6% S250A (TCG→GCG)  cynR_3 ← HTH‑type transcriptional regulator CynR
RA 3,404,075 A→G 5.5% N350S (AAT→AGT)  CJ019_03222 → hypothetical protein
RA 3,413,147 T→G 24.4% D2A (GAC→GCC)  lexA_2 ← LexA repressor
RA 3,436,622 A→C 45.4% E775A (GAG→GCG)  CJ019_03261 → hypothetical protein
RA 3,490,632 G→A 8.3% Q3* (CAG→TAG)  CJ019_03306 ← hypothetical protein
RA 3,532,861 A→G 7.4% K164R (AAG→AGG)  CJ019_03352 → hypothetical protein
RA 3,731,291 T→A 17.1% intergenic (+38/‑14) cnrA → / → fabF_3 Nickel and cobalt resistance protein CnrA/3‑oxoacyl‑[acyl‑carrier‑protein] synthase 2
RA 3,879,284 A→G 6.9% E508E (GAA→GAG rcsC_8 → Sensor histidine kinase RcsC
RA 3,986,622 T→G 38.5% D31A (GAT→GCT)  CJ019_03763 ← hypothetical protein
RA 4,124,901 C→T 7.9% G234R (GGG→AGG)  CJ019_03883 ← hypothetical protein
RA 4,134,647 T→G 17.0% intergenic (+33/‑36) CJ019_03892 → / → tgnD hypothetical protein/(E)‑2‑((N‑methylformamido)methylene)succinatehydr olase
RA 4,245,145 A→C 34.3% L178R (CTG→CGG)  CJ019_03982 ← Crotonyl‑CoA hydratase
RA 4,247,323 T→C 5.3% M1V (ATG→GTG) † rocE ← Amino‑acid permease RocE
JC 4,257,351 +CGCGGCCG 100% intergenic (‑280/+8) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,271,001 T→C 6.1% L196P (CTG→CCG)  gabR_1 → HTH‑type transcriptional regulatory proteinGabR
RA 4,341,371 G→C 14.0% D64E (GAC→GAG gtaB ← UTP‑‑glucose‑1‑phosphate uridylyltransferase
RA 4,342,664 T→G 34.7% Q17P (CAG→CCG)  tsdA ← Thiosulfate dehydrogenase
RA 4,415,941 G→A 6.0% P80P (CCG→CCA CJ019_04188 → hypothetical protein
RA 4,539,411 Δ1 bp 6.6% coding (109/1440 nt) dht → D‑hydantoinase/dihydropyrimidinase
RA 4,591,760 Δ1 bp 5.8% coding (1128/1467 nt) CJ019_04341 ← hypothetical protein
RA 4,609,122 G→A 5.2% D1293N (GAC→AAC)  CJ019_04355 → hypothetical protein
RA 4,654,316 A→C 22.6% N522H (AAC→CAC)  nuoG → NADH‑quinone oxidoreductase subunit G
RA 4,789,585 A→C 26.5% V230G (GTG→GGG)  dat ← Diaminobutyrate‑‑2‑oxoglutarateaminotransferase
RA 4,851,374 A→T 6.9% F153Y (TTC→TAC)  CJ019_04550 ← hypothetical protein
MC JC 4,963,095 Δ12,336 bp 100% [CJ019_04659][flgE] [CJ019_04659], fabH, CJ019_04661, CJ019_04662, CJ019_04663, flgI, flgH, flgG, flgF, CJ019_04668, [flgE]
RA 5,119,340 T→G 26.5% G55G (GGT→GGG CJ019_04815 → hypothetical protein
RA 5,201,776 G→A 6.4% R301W (CGG→TGG)  ghrA ← Glyoxylate/hydroxypyruvate reductase A
RA 5,226,991 T→G 9.8% intergenic (‑26/‑132) CJ019_04921 ← / → fecI_10 hypothetical protein/putative RNA polymerase sigma factor FecI
RA 5,264,429 C→T 5.9% intergenic (‑123/‑54) radA ← / → mscL DNA repair protein RadA/Large‑conductance mechanosensitive channel
RA 5,270,972 C→T 6.8% intergenic (‑308/‑36) cydA ← / → entS_1 Cytochrome bd‑I ubiquinol oxidase subunit 1/Enterobactin exporter EntS
RA 5,284,855 T→G 18.8% F162C (TTT→TGT)  cmpR_6 → HTH‑type transcriptional activator CmpR
RA 5,358,465 T→G 22.4% E46A (GAG→GCG)  folP ← Dihydropteroate synthase
RA 5,613,064 C→T 6.3% P13P (CCG→CCA mshA_6 ← D‑inositol‑3‑phosphate glycosyltransferase
RA 5,756,055 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 5,787,816 A→C 17.1% F914V (TTT→GTT)  gltB ← Glutamate synthase [NADPH] large chain
RA 5,883,454 C→G 19.0% intergenic (+86/+34) quiP → / ← metQ_2 Acyl‑homoserine lactone acylase QuiP/putative D‑methionine‑binding lipoprotein MetQ
RA 5,927,532 A→C 39.9% intergenic (+111/‑104) PP_RS08755 → / → ygfA tRNA‑Asp/5‑formyltetrahydrofolate cyclo‑ligase
RA 6,002,324 G→T 6.6% D395E (GAC→GAA CJ019_05620 ← hypothetical protein
RA 6,025,859 A→G 5.8% L126P (CTC→CCC)  CJ019_05642 ← hypothetical protein
RA 6,038,652 A→C 27.1% L39V (TTG→GTG)  puuD_3 ← Gamma‑glutamyl‑gamma‑aminobutyrate hydrolasePuuD
RA 6,102,900 G→A 6.7% L21L (CTG→TTG)  CJ019_05717 ← hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB122 80702 80854 153 18 [17] [17] 18 [gcvA_2] [gcvA_2]
* * ÷ ACB122 87973 88052 80 18 [17] [17] 21 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB122 161227 161447–161315 89–221 18 [17] [17] 19 [uctC_1] [uctC_1]
* * ÷ ACB122 213570 213694 125 21 [17] [17] 19 [CJ019_00185] [CJ019_00185]
* * ÷ ACB122 517190 517274 85 27 [16] [15] 18 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB122 674236 674385 150 18 [17] [17] 19 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB122 690120 690245 126 18 [17] [16] 18 [bauC] [bauC]
* * ÷ ACB122 1106825 1106930 106 19 [17] [17] 18 [hupB_1]–[rlmF] [hupB_1],[rlmF]
* * ÷ ACB122 1304752 1304856 105 19 [17] [16] 18 CJ019_01223/rapA putative signaling protein/RNA polymerase‑associated protein RapA
* * ÷ ACB122 1457218 1457299 82 19 [17] [16] 18 [algL]–[algX] [algL],[algX]
* * ÷ ACB122 1585616 1585714 99 21 [17] [16] 18 CJ019_01493 hypothetical protein
* * ÷ ACB122 1608712 1608816 105 18 [16] [17] 19 [CJ019_01513]–[CJ019_01514] [CJ019_01513],[CJ019_01514]
* * ÷ ACB122 1697667 1697754 88 18 [11] [17] 18 [CJ019_01593]–[CJ019_01594] [CJ019_01593],[CJ019_01594]
* * ÷ ACB122 1705092 1705211 120 19 [15] [17] 18 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB122 1914565 1914669 105 20 [17] [17] 18 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB122 1923416 1923505 90 18 [16] [14] 19 [apeB] [apeB]
* * ÷ ACB122 1940819 1940915 97 18 [17] [13] 18 CJ019_01857/gshAB hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB
* * ÷ ACB122 2031249 2031437 189 19 [17] [15] 18 [wecB] [wecB]
* * ÷ ACB122 2092983 2093085 103 18 [16] [17] 19 rcsC_3/CJ019_01993 Sensor histidine kinase RcsC/hypothetical protein
* * ÷ ACB122 2234310 2234415 106 19 [17] [15] 18 [gltX] [gltX]
* * ÷ ACB122 3046178 3046347 170 18 [17] [16] 22 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB122 3769400 3769474 75 18 [16] [16] 19 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB122 3839304 3839419 116 20 [17] [17] 20 [argP_2] [argP_2]
* * ÷ ACB122 4025777 4025854 78 18 [14] [17] 18 dmdC_5/CJ019_03801 3‑methylmercaptopropionyl‑CoA dehydrogenase/hypothetical protein
* * ÷ ACB122 4107958 4108006 49 18 [16] [12] 19 CJ019_03867/ycaO hypothetical protein/Ribosomal protein S12 methylthiotransferaseaccessory factor YcaO
* * ÷ ACB122 4163777 4163890 114 18 [16] [17] 18 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB122 4330066 4330132 67 18 [16] [17] 18 aes/CJ019_04068 Acetyl esterase/hypothetical protein
* * ÷ ACB122 4331594 4331740 147 18 [17] [13] 18 [ribBA_2] [ribBA_2]
* * ÷ ACB122 4344773 4344825 53 18 [15] [15] 20 nmoA Nitronate monooxygenase
* * ÷ ACB122 4495363 4495449 87 18 [17] [17] 18 [xanP]–[dsrE] [xanP],[dsrE]
* * ÷ ACB122 4521608 4521703 96 19 [17] [16] 20 [CJ019_04289] [CJ019_04289]
* * ÷ ACB122 4666863 4667006 144 18 [17] [17] 18 [btuB_4] [btuB_4]
* * ÷ ACB122 4732398 4732488 91 19 [15] [17] 18 gltA/CJ019_04468 Citrate synthase/hypothetical protein
* * ÷ ACB122 4846395 4846501 107 18 [15] [16] 20 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB122 4944867 4945037 171 18 [17] [17] 19 [CJ019_04642] [CJ019_04642]
* * ÷ ACB122 5156429 5156590 162 20 [17] [16] 18 [CJ019_04852] [CJ019_04852]
* * ÷ ACB122 5193555 5193691 137 18 [12] [15] 22 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB122 5250773 5250871 99 18 [17] [15] 22 [CJ019_04947]–[CJ019_04948] [CJ019_04947],[CJ019_04948]
* * ÷ ACB122 5499088 5499274 187 19 [17] [17] 18 [CJ019_05176] [CJ019_05176]
* * ÷ ACB122 5645609 5645691 83 24 [16] [17] 19 CJ019_05302/CJ019_05303 hypothetical protein/hypothetical protein
* * ÷ ACB122 5674000 5674123 124 20 [15] [17] 19 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB122 5890354 5890478 125 22 [17] [17] 18 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ ACB122 5895768 5895851 84 18 [17] [16] 18 [CJ019_05521] [CJ019_05521]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB122 = 293402940 (0.710)8 (0.140) 7/232 NT 15.4% coding (204/912 nt) gltC_3 HTH‑type transcriptional regulator GltC
?ACB122 3005553 = 48 (0.870)coding (1557/1614 nt) bcsG Cellulose biosynthesis protein BcsG
* ? ACB122 4383137 =NA (NA)5 (0.090) 5/232 NT 5.9% intergenic (‑13/+70) CJ019_04133/CJ019_00698 hypothetical protein/hypothetical protein
?ACB122 = 5388386 80 (1.430)intergenic (‑1746/‑36) CJ019_05070/CJ019_05072 hypothetical protein/hypothetical protein
* ? ACB122 = 598141331 (0.550)5 (0.100) 5/218 NT 15.2% intergenic (+51/‑638) kefC_3/CJ019_05604 Glutathione‑regulated potassium‑efflux systemprotein KefC/hypothetical protein
?ACB122 5981635 = 27 (0.520)intergenic (+273/‑416) kefC_3/CJ019_05604 Glutathione‑regulated potassium‑efflux systemprotein KefC/hypothetical protein