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 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 195,703 C→T 6.2% S3521L (TCG→TTG)  CJ019_00185 → hypothetical protein
RA 546,499 A→G 89.8% intergenic (+11/‑6) rplB → / → rpsS 50S ribosomal protein L2/30S ribosomal protein S19
RA 659,271 C→G 6.0% R1029R (CGC→CGG)  yfhM → Alpha‑2‑macroglobulin
RA 690,144 A→G 100% intergenic (+21/‑2438) bauC → / → PP_RS08750 Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val
RA 690,150 T→G 100% intergenic (+27/‑2432) bauC → / → PP_RS08750 Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val
RA 690,162 G→C 100% intergenic (+39/‑2420) bauC → / → PP_RS08750 Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val
RA 733,847 C→T 92.3% intergenic (‑171/‑46) epsF ← / → pilA Type II secretion system protein F/Fimbrial protein
RA 838,759 G→T 12.9% I94I (ATC→ATA)  CJ019_00802 ← L‑glutamine kinase
RA 1,005,859 G→A 7.3% K407K (AAG→AAA)  prfC → Peptide chain release factor RF3
RA 1,141,856 C→G 49.3% D97H (GAC→CAC)  CJ019_01079 ← hypothetical protein
RA 1,166,671 T→C 6.7% E136E (GAA→GAG)  hcaR_1 ← Hca operon transcriptional activator HcaR
RA 1,272,812 A→T 6.8% R79R (CGT→CGA)  CJ019_01194 ← hypothetical protein
RA 1,302,662 G→A 7.0% R642C (CGC→TGC)  CJ019_01223 ← putative signaling protein
RA 1,310,036:1 +C 100% coding (401/1989 nt) aaeB_2 → p‑hydroxybenzoic acid efflux pump subunit AaeB
RA 1,513,723 C→T 86.2% P336L (CCC→CTC)  mraY → Phospho‑N‑acetylmuramoyl‑pentapeptide‑transferas e
RA 1,587,077 A→G 9.9% intergenic (‑219/+82) CJ019_01495 ← / ← kgtP_2 hypothetical protein/Alpha‑ketoglutarate permease
RA 1,721,874 A→C 34.9% W97G (TGG→GGG)  CJ019_01617 ← hypothetical protein
RA 1,835,796 1 bp→TT 100% coding (2054/2754 nt) barA ← Signal transduction histidine‑protein kinaseBarA
RA 2,042,793 T→C 9.1% E47E (GAA→GAG)  folE_1 ← GTP cyclohydrolase 1
RA 2,094,808 A→C 49.1% L186R (CTG→CGG)  CJ019_01995 ← hypothetical protein
RA 2,094,817 T→G 37.0% Q183P (CAG→CCG)  CJ019_01995 ← hypothetical protein
RA 2,134,614 G→A 8.9% A431A (GCG→GCA)  comEC → ComE operon protein 3
RA 2,171,211 T→A 9.1% R130R (CGT→CGA)  CJ019_02060 → IS1182 family transposase ISPpu16
RA 2,171,262 C→A 9.3% F147L (TTC→TTA)  CJ019_02060 → IS1182 family transposase ISPpu16
RA 2,171,266 G→C 13.8% A149P (GCA→CCA)  CJ019_02060 → IS1182 family transposase ISPpu16
RA 2,176,936 C→A 12.9% intergenic (+110/‑64) CJ019_02067 → / → CJ019_02068 hypothetical protein/Tn3 family transposase ISYps3
JC 2,191,046 +CTGAAAATATCTCTTAT 100% intergenic (‑1/‑313) PP_RS10045 ← / → purU_3 LysR family transcriptional regulator/Formyltetrahydrofolate deformylase
RA 2,353,513 G→A 13.3% G227G (GGC→GGT)  CJ019_02227 ← hypothetical protein
RA 2,353,557 G→A 8.4% L213L (CTG→TTG)  CJ019_02227 ← hypothetical protein
RA 2,434,427 T→C 100% R175R (CGT→CGC)  topA → DNA topoisomerase 1
RA 2,847,248 A→G 100% intergenic (+20/‑26) CJ019_02702 → / → CJ019_02703 hypothetical protein/hypothetical protein
RA 2,883,291 C→A 11.8% T420N (ACC→AAC)  gabP_2 → GABA permease
RA 3,214,279 G→A 20.5% I474I (ATC→ATT)  CJ019_03017 ← hypothetical protein
RA 3,267,793 T→G 27.8% L171V (TTG→GTG)  eamA → putative amino‑acid metabolite efflux pump
RA 3,387,164 C→T 87.3% A95T (GCC→ACC)  pcpR_4 ← PCP degradation transcriptional activationprotein
RA 3,448,459 C→T 9.2% A158T (GCC→ACC)  acsA_3 ← Acetyl‑coenzyme A synthetase
RA 3,615,019 T→C 7.3% H20R (CAC→CGC)  dauR_2 ← Transcriptional regulator DauR
RA 3,860,407 A→G 15.1% R33R (CGT→CGC)  gntR_2 ← HTH‑type transcriptional regulator GntR
RA 3,900,666 C→T 65.7% A508V (GCC→GTC)  CJ019_03690 → hypothetical protein
RA 4,245,128 A→C 31.9% 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 4,672,065 C→T 8.9% E94K (GAG→AAG)  CJ019_04415 ← hypothetical protein
RA 4,759,509 G→A 100% intergenic (+124/‑16) fpvA_3 → / → ligM_KToptimized Ferripyoverdine receptor/sequence generated by OPTIMIZER for KT2440
RA 4,788,936 A→C 14.7% V230G (GTG→GGG)  dat ← Diaminobutyrate‑‑2‑oxoglutarateaminotransferase
RA 4,807,149 G→C 12.0% S66T (AGC→ACC)  mcbC → Microcin B17‑processing protein McbC
RA 4,807,160 G→C 11.6% E70Q (GAA→CAA)  mcbC → Microcin B17‑processing protein McbC
RA 5,009,212 Δ1 bp 100% intergenic (‑156/+78) CJ019_04705 ← / ← spuC_5 hypothetical protein/Putrescine‑‑pyruvate aminotransferase
RA 5,124,825 A→G 85.1% intergenic (‑103/‑141) recQ ← / → CJ019_04820 ATP‑dependent DNA helicase RecQ/hypothetical protein
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 5,390,191 Δ10 bp 16.8% coding (285‑294/1666 nt) ligH → 10‑formyltetrahydrofolate synthetase
RA 5,390,258 Δ2 bp 100% coding (352‑353/1666 nt) ligH → 10‑formyltetrahydrofolate synthetase
RA 5,391,491 G→T 6.2% G529C (GGC→TGC)  ligH → 10‑formyltetrahydrofolate synthetase
JC 5,391,707 +54 bp 100% intergenic (+124/‑1253) ligH → / → CJ019_05072 10‑formyltetrahydrofolate synthetase/hypothetical protein
RA 5,497,877 A→T 8.0% Y53F (TAC→TTC)  qmcA → Protein QmcA
RA 5,507,078 A→C 44.5% E31A (GAG→GCG)  CJ019_05179 → hypothetical protein
RA 5,760,593 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 6,129,757 A→T 26.3% H430Q (CAT→CAA)  copA_4 ← Copper resistance protein A

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB143 161233 161409–161317 85–177 10 [9] [9] 11 [uctC_1] [uctC_1]
* * ÷ ACB143 277601 277660 60 11 [9] [8] 11 [betT2] [betT2]
* * ÷ ACB143 492246 492319 74 10 [9] [9] 11 uvrY/potA_1 Response regulator UvrY/Spermidine/putrescine import ATP‑binding proteinPotA
* * ÷ ACB143 517195 517276 82 10 [6] [8] 12 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB143 661111 661215 105 10 [9] [9] 10 yfhM/CJ019_00619 Alpha‑2‑macroglobulin/hypothetical protein
* * ÷ ACB143 674272 674380 109 11 [8] [8] 10 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB143 711484 711556 73 10 [9] [9] 12 thiO/aam Glycine oxidase/Acylamidase
* * ÷ ACB143 876896 876940 45 10 [9] [8] 10 CJ019_00843/malT putative protein/HTH‑type transcriptional regulator MalT
* * ÷ ACB143 1376293 1376321 29 10 [6] [9] 12 CJ019_01289 hypothetical protein
* * ÷ ACB143 1396604 1396658 55 10 [9] [9] 10 CJ019_01313/mcpU_1 hypothetical protein/Methyl‑accepting chemotaxis protein McpU
* * ÷ ACB143 1585612 1585704 93 10 [9] [8] 10 CJ019_01493 hypothetical protein
* * ÷ ACB143 1697665 1697726 62 10 [9] [9] 10 [CJ019_01593] [CJ019_01593]
* * ÷ ACB143 1705077 1705214 138 10 [8] [8] 11 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB143 1940824 1940935 112 10 [9] [9] 10 CJ019_01857/gshAB hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB
* * ÷ ACB143 2288819 2288919 101 10 [9] [9] 11 CJ019_02171/CJ019_02172 hypothetical protein/hypothetical protein
* * ÷ ACB143 2646594 2646746 153 10 [9] [9] 10 [CJ019_02505]–[CJ019_02506] [CJ019_02505],[CJ019_02506]
* * ÷ ACB143 2897501 2897645 145 10 [9] [8] 10 CJ019_02754 hypothetical protein
* * ÷ ACB143 3046213 3046335 123 10 [9] [8] 10 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB143 3145306 3145367 62 10 [8] [7] 10 livH_4 High‑affinity branched‑chain amino acidtransport system permease protein LivH
* * ÷ ACB143 3769377 3769465 89 10 [8] [9] 10 CJ019_03581/CJ019_03582 hypothetical protein/hypothetical protein
* * ÷ ACB143 4163785 4163873 89 12 [7] [9] 10 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB143 4331636 4331733 98 11 [8] [9] 10 ribBA_2/potD_2 Riboflavin biosynthesis protein RibBA/Spermidine/putrescine‑binding periplasmicprotein
* * ÷ ACB143 4335859 4335949 91 10 [8] [9] 10 [btuD_7] [btuD_7]
* * ÷ ACB143 4344757 4344818 62 12 [9] [8] 10 nmoA Nitronate monooxygenase
* * ÷ ACB143 4521592 4521660 69 11 [8] [9] 10 CJ019_04289/topB Acetyltransferase/DNA topoisomerase 3
* * ÷ ACB143 4666891 4666980 90 11 [9] [4] 13 [btuB_4] [btuB_4]
* * ÷ ACB143 4732414 4732479 66 10 [7] [7] 10 [CJ019_04468] [CJ019_04468]
* * ÷ ACB143 4836194 4836248 55 11 [9] [9] 10 ccoP2_2/CJ019_04535 Cbb3‑type cytochrome c oxidase subunit CcoP2/hypothetical protein
* * ÷ ACB143 4845743 4845801 59 10 [9] [9] 10 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB143 4944222 4944330 109 10 [9] [8] 10 [CJ019_04642] [CJ019_04642]
* * ÷ ACB143 5090543 5090602 60 10 [7] [9] 10 argT/acs Lysine/arginine/ornithine‑binding periplasmicprotein/Acetyl‑coenzyme A synthetase
* * ÷ ACB143 5250147 5250222 76 11 [9] [9] 10 [CJ019_04947]–[CJ019_04948] [CJ019_04947],[CJ019_04948]
* * ÷ ACB143 5337749 5337842 94 10 [9] [8] 10 pgi_2/acsA_4 Glucose‑6‑phosphate isomerase/Acetyl‑coenzyme A synthetase
* * ÷ ACB143 5482310 5482387 78 10 [9] [7] 10 purH/purD Bifunctional purine biosynthesis protein PurH/Phosphoribosylamine‑‑glycine ligase
* * ÷ ACB143 5503642 5503801 160 12 [9] [9] 10 [CJ019_05176] [CJ019_05176]
* * ÷ ACB143 5534210 5534285 76 10 [9] [9] 10 nadE/CJ019_05208 NH(3)‑dependent NAD( ) synthetase/Azurin
* * ÷ ACB143 5678567 5678650 84 10 [9] [9] 10 CJ019_05328/CJ019_05329 hypothetical protein/hypothetical protein
* * ÷ ACB143 5900315 5900387 73 13 [9] [5] 10 [CJ019_05521] [CJ019_05521]
* * ÷ ACB143 6078152 6078220 69 11 [9] [5] 10 [CJ019_05690] [CJ019_05690]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? ACB143 2155685 =43 (0.970)143 (3.240) 49/242 NT 79.2% coding (301/369 nt) tmk_1 Thymidylate kinase
?ACB143 = 2220562 32 (0.730)coding (36/369 nt) tmk_2 Thymidylate kinase
* ? ACB143 2170758 =126 (2.860)35 (0.810) 23/238 NT 34.8% intergenic (‑773/‑64) arsR1/CJ019_02060 Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16
?ACB143 5563630 = 7 (0.160)coding (1047/1902 nt) mutL_2 DNA mismatch repair protein MutL
* ? ACB143 = 2172434148 (3.360)37 (0.850) 24/240 NT 32.5% intergenic (+176/+92) CJ019_02060/CJ019_02061 IS1182 family transposase ISPpu16/hypothetical protein
?ACB143 = 5563631 7 (0.160)coding (1046/1902 nt) mutL_2 DNA mismatch repair protein MutL
* ? ACB143 = 29307270 (0.000)36 (0.830) 15/238 NT 100% intergenic (+44/+39) nanT_2/CJ019_02768 Sialic acid transporter NanT/IS110 family transposase ISPpu9
?ACB143 3819889 = NA (NA)intergenic (‑13/+386) CJ019_03622/CJ019_02768 IS110 family transposase ISPpu9/IS110 family transposase ISPpu9
* ? ACB143 3359593 =24 (0.540)133 (3.010) 62/242 NT 90.8% intergenic (+219/‑151) pikAII_1/CJ019_03160 Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42
?ACB143 4735167 = 3 (0.070)coding (274/1443 nt) hisC_7 Histidinol‑phosphate aminotransferase
* ? ACB143 = 337660546 (1.040)41 (0.930) 27/242 NT 62.6% coding (501/546 nt) CJ019_03184 hypothetical protein
?ACB143 = 4735171 3 (0.070)coding (270/1443 nt) hisC_7 Histidinol‑phosphate aminotransferase
* ? ACB143 = 337660546 (1.040)74 (1.680) 37/242 NT 66.1% coding (501/546 nt) CJ019_03184 hypothetical protein
?ACB143 = 4825543 30 (0.680)coding (964/1014 nt) CJ019_04522 hypothetical protein