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 96,480 T→G 25.7% 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 179,484 T→C 100% C316R (TGC→CGC)  CJ019_00182 → hypothetical protein
RA 233,250 A→C 22.4% K157N (AAA→AAC hemX → Protein HemX
RA 381,772 T→G 23.5% L198R (CTG→CGG)  soxB → Sarcosine oxidase subunit beta
RA 399,292 A→C 35.6% intergenic (‑186/+122) CJ019_00365 ← / ← aceF hypothetical protein/Dihydrolipoyllysine‑residue acetyltransferasecomponent of pyruvate dehydrogenase complex
RA 444,535 A→C 24.7% L130V (TTG→GTG)  hdfR_1 ← HTH‑type transcriptional regulator HdfR
RA 464,193 A→G 7.5% L598L (TTG→CTG)  rpoD ← RNA polymerase sigma factor RpoD
RA 478,881 A→C 22.2% V35G (GTC→GGC)  apaH_1 ← Bis(5'‑nucleosyl)‑tetraphosphatase, symmetrical
RA 570,448 A→C 39.8% D599A (GAC→GCC)  fdoG_2 → Formate dehydrogenase‑O major subunit
RA 613,718 C→G 8.7% A8P (GCC→CCC)  ompR_3 ← Transcriptional regulatory protein OmpR
RA 624,906 A→C 27.1% intergenic (‑164/+64) potE ← / ← adh_1 Putrescine transporter PotE/Aldehyde dehydrogenase
RA 953,823 T→G 17.6% K203T (AAG→ACG)  selU ← tRNA 2‑selenouridine synthase
RA 999,352 G→A 8.0% R411Q (CGG→CAG)  fecA_1 → Fe(3 ) dicitrate transport protein FecA
RA 1,125,327 C→A 6.1% L13L (CTG→CTT CJ019_01064 ← hypothetical protein
RA 1,188,694 T→G 46.3% L43R (CTG→CGG)  CJ019_01117 → hypothetical protein
RA 1,196,474 T→G 17.3% G55G (GGT→GGG CJ019_01126 → hypothetical protein
RA 1,202,727 G→A 7.8% G95S (GGC→AGC)  proY_1 → Proline‑specific permease ProY
RA 1,205,992 A→G 7.8% P1340P (CCT→CCC rhlB_1 ← ATP‑dependent RNA helicase RhlB
RA 1,212,593 G→T 5.5% G312G (GGG→GGT rdmC_1 → Aclacinomycin methylesterase RdmC
RA 1,313,943 A→C 40.7% L614R (CTG→CGG)  CJ019_01235 ← hypothetical protein
RA 1,408,984 G→C 5.5% G101R (GGC→CGC)  bamC → Outer membrane protein assembly factor BamC
RA 1,464,306 T→G 17.9% Q16P (CAG→CCG)  CJ019_01381 ← Mannuronan synthase
RA 1,472,154 T→G 27.9% V55G (GTG→GGG)  moaC → Cyclic pyranopterin monophosphate synthase
RA 1,503,076 G→A 69.1% P516L (CCG→CTG)  lpoA ← Penicillin‑binding protein activator LpoA
RA 1,544,643 T→G 36.2% Q412P (CAG→CCG)  pykA ← Pyruvate kinase II
RA 1,585,043 T→G 32.3% intergenic (‑94/‑109) rhaS_1 ← / → CJ019_01492 HTH‑type transcriptional activator RhaS/hypothetical protein
RA 1,630,540 A→C 42.8% L419R (CTG→CGG)  czcS ← Sensor protein CzcS
RA 1,670,696 A→C 22.0% intergenic (+33/‑98) thrC_2 → / → CJ019_01569 Threonine synthase/hypothetical protein
RA 1,674,731 A→C 35.9% D65A (GAC→GCC)  recJ → Single‑stranded‑DNA‑specific exonuclease RecJ
RA 1,687,834 C→G 5.5% G248G (GGC→GGG wspC → putative biofilm formation methyltransferaseWspC
RA 1,718,463 T→G 32.9% Q65P (CAG→CCG)  CJ019_01614 ← hypothetical protein
RA 1,720,951 T→G 35.7% D90A (GAC→GCC)  plsB ← Glycerol‑3‑phosphate acyltransferase
RA 1,721,870 A→C 21.5% V98G (GTC→GGC)  CJ019_01617 ← hypothetical protein
RA 1,791,678 T→G 32.8% L182R (CTG→CGG)  lpxB → Lipid‑A‑disaccharide synthase
RA 1,828,161 G→T 7.3% R152R (CGG→AGG)  sprT ← Protein SprT
RA 1,856,481 G→A 5.4% G11S (GGC→AGC)  CJ019_01772 → Sodium‑lithium/proton antiporter
RA 1,861,266 A→C 32.4% A108A (GCA→GCC cbiA → Cobyrinate a,c‑diamide synthase
RA 1,862,899 G→T 6.2% L6L (CTG→CTT cobD → Cobalamin biosynthesis protein CobD
RA 1,892,407 A→C 29.6% intergenic (+421/‑99) PP_RS08755 → / → napA tRNA‑Asp/Periplasmic nitrate reductase
RA 2,003,336 C→A 7.2% W385C (TGG→TGT CJ019_01904 ← hypothetical protein
RA 2,037,270 C→G 5.6% E57Q (GAA→CAA)  CJ019_01932 ← hypothetical protein
RA 2,118,179 A→T 5.7% S164C (AGT→TGT)  CJ019_02010 → hypothetical protein
RA 2,134,732 T→G 20.7% L471V (TTG→GTG)  comEC → ComE operon protein 3
RA 2,308,600 C→G 5.5% A137P (GCC→CCC)  fucA ← L‑fuculose phosphate aldolase
RA 2,608,168 G→T 6.3% W1350C (TGG→TGT CJ019_02463 → hypothetical protein
RA 2,636,079 A→G 6.1% T429A (ACC→GCC)  mltF_2 → Membrane‑bound lytic murein transglycosylase F
RA 2,652,493 T→C 5.1% E300E (GAA→GAG CJ019_02511 ← hypothetical protein
RA 2,696,522 C→T 8.5% Q208* (CAG→TAG)  CJ019_02551 → hypothetical protein
RA 2,758,087 T→G 24.0% intergenic (‑113/+225) CJ019_02600 ← / ← CJ019_02602 hypothetical protein/hypothetical protein
RA 2,805,671 G→C 6.4% E89Q (GAA→CAA)  rplT → 50S ribosomal protein L20
RA 2,880,012 G→T 6.5% T13T (ACC→ACA CJ019_02740 ← hypothetical protein
RA 3,003,619 G→A 6.0% D311N (GAC→AAC)  bcsE → Cyclic di‑GMP binding protein BcsE
RA 3,044,626 A→C 50.4% E90A (GAG→GCG)  rcsC_5 → Sensor histidine kinase RcsC
RA 3,047,211 T→G 21.6% K124N (AAA→AAC CJ019_02862 ← hypothetical protein
RA 3,065,508 G→A 89.1% V53M (GTG→ATG)  rcsC_6 → Sensor histidine kinase RcsC
RA 3,162,433 C→T 8.5% A421V (GCC→GTC)  argD_2 → Acetylornithine/succinyldiaminopimelateaminotrans ferase
RA 3,176,299 G→A 9.0% R301H (CGT→CAT)  carC_2 → Caffeyl‑CoA reductase‑Etf complex subunit CarC
RA 3,228,754 C→T 7.5% R264R (CGC→CGT garD_1 → Galactarate dehydratase (L‑threo‑forming)
RA 3,274,993 T→A 12.7% V153E (GTA→GAA)  nsaD → 2‑hydroxychromene‑2‑carboxylate isomerase
RA 3,308,725 A→C 27.6% L164R (CTG→CGG)  CJ019_03110 ← hypothetical protein
RA 3,388,835 C→T 5.6% A112V (GCG→GTG)  CJ019_03197 → hypothetical protein
RA 3,440,343 A→C 100% S18R (AGC→CGC)  CJ019_03266 → hypothetical protein
RA 3,465,424 T→G 21.6% A41A (GCA→GCC fcuA_1 ← Ferrichrome receptor FcuA
RA 3,475,364 C→A 8.0% R1206L (CGG→CTG)  CJ019_03296 ← hypothetical protein
RA 3,483,024 G→A 7.0% A462V (GCC→GTC)  clpV1 ← Protein ClpV1
RA 3,491,323 T→G 51.2% intergenic (‑685/+36) CJ019_03306 ← / ← CJ019_03307 hypothetical protein/hypothetical protein
RA 3,572,268 C→T 6.3% T33T (ACG→ACA CJ019_03385 ← hypothetical protein
RA 3,580,395 C→T 6.4% A58A (GCC→GCT catA_1 → Catechol 1,2‑dioxygenase
RA 3,703,189 T→C 5.4% K89E (AAG→GAG)  paaE ← 1,2‑phenylacetyl‑CoA epoxidase, subunit E
RA 3,851,026 C→T 5.6% R145R (CGC→CGT CJ019_03648 → hypothetical protein
RA 3,857,773 Δ1 bp 6.9% coding (3051/3282 nt) rcsC_7 → Sensor histidine kinase RcsC
RA 3,875,885 A→C 23.4% N300T (AAC→ACC)  ttgI_2 → Toluene efflux pump outer membrane protein TtgI
RA 3,931,996 A→G 5.0% D118G (GAT→GGT)  CJ019_03714 → hypothetical protein
RA 3,957,240 C→T 100% G137R (GGG→AGG)  dmlR_13 ← HTH‑type transcriptional regulator DmlR
RA 3,977,481 A→C 44.5% T284P (ACC→CCC)  ilvE → Branched‑chain‑amino‑acid aminotransferase
RA 3,986,622 T→G 29.8% D31A (GAT→GCT)  CJ019_03763 ← hypothetical protein
RA 4,004,497 G→A 9.1% W20* (TGG→TGA rhaR_6 → HTH‑type transcriptional activator RhaR
RA 4,146,293 G→A 6.7% A192A (GCC→GCT nicP_9 ← Porin‑like protein NicP
RA 4,180,181 C→T 5.7% intergenic (+655/‑175) uvrD_1 → / → CJ019_03928 DNA helicase II/hypothetical protein
RA 4,245,145 A→C 49.3% L178R (CTG→CGG)  CJ019_03982 ← Crotonyl‑CoA hydratase
RA 4,249,801 C→T 7.1% D251N (GAC→AAC)  CJ019_03985 ← hypothetical protein
JC 4,257,351 +CGCGGCCG 100% intergenic (‑280/+8) CJ019_03991 ← / ← CJ019_03994 putative ABC transporter ATP‑binding protein/hypothetical protein
RA 4,403,899 A→T 5.1% E108V (GAA→GTA)  CJ019_04165 → hypothetical protein
RA 4,500,213 A→C 44.4% L61R (CTG→CGG)  cysG_1 ← Siroheme synthase
RA 4,687,945 A→G 5.1% intergenic (‑46/‑45) CJ019_04426 ← / → yhaJ_2 hypothetical protein/HTH‑type transcriptional regulator YhaJ
RA 4,711,854 G→A 8.2% L109L (CTG→CTA CJ019_04448 → hypothetical protein
RA 4,742,598 G→A 6.4% P397L (CCG→CTG)  proP_5 ← Proline/betaine transporter
RA 4,940,742 G→C 8.2% L195V (CTG→GTG)  fliR ← Flagellar biosynthetic protein FliR
RA 4,994,820 G→T 8.2% intergenic (+322/‑62) gabP_5 → / → CJ019_04690 GABA permease/IS5 family transposase ISPsp10
RA 5,009,692 G→C 7.3% A5G (GCT→GGT)  CJ019_04705 ← hypothetical protein
RA 5,083,473 C→T 6.3% A112T (GCC→ACC)  aruG ← Arginine N‑succinyltransferase subunit beta
RA 5,086,965 T→C 6.1% K209E (AAG→GAG)  cdhR_7 ← HTH‑type transcriptional regulator CdhR
RA 5,247,863 T→G 30.9% R255R (AGG→CGG)  CJ019_04943 ← hypothetical protein
RA 5,334,835 A→T 19.2% intergenic (+236/‑27) folK → / → panB 2‑amino‑4‑hydroxy‑6‑hydroxymethyldihydropteridine pyrophosphokinase/3‑methyl‑2‑oxobutanoatehydroxymethyltransferase
RA 5,359,751 A→G 7.5% I258T (ATC→ACC)  ftsH ← ATP‑dependent zinc metalloprotease FtsH
RA 5,381,985 C→T 6.2% I509I (ATC→ATT CJ019_05063 → hypothetical protein
RA 5,409,654 A→G 8.2% L226P (CTG→CCG)  gudD ← Glucarate dehydratase
RA 5,423,488 A→C 13.3% S133A (TCG→GCG)  CJ019_05102 ← hypothetical protein
RA 5,438,375 G→A 8.0% L228L (TTG→TTA thiD → Hydroxymethylpyrimidine/phosphomethylpyrimidineki nase
RA 5,471,653 G→A 5.3% intergenic (‑132/‑12) cidA_2 ← / → CJ019_05151 Holin‑like protein CidA/putative enoyl‑CoA hydratase 1
RA 5,471,660 C→T 5.2% intergenic (‑139/‑5) cidA_2 ← / → CJ019_05151 Holin‑like protein CidA/putative enoyl‑CoA hydratase 1
RA 5,559,702 A→C 35.7% V146G (GTC→GGC)  mutL_2 ← DNA mismatch repair protein MutL
RA 5,562,567 A→C 20.0% L132R (CTG→CGG)  nnr ← Bifunctional NAD(P)H‑hydrate repair enzyme Nnr
RA 5,646,451 G→A 7.0% A225V (GCC→GTC)  pgk ← Phosphoglycerate kinase
RA 5,656,106 A→C 21.4% K68T (AAG→ACG)  mltA → Membrane‑bound lytic murein transglycosylase A
RA 5,688,615 T→G 44.3% R228R (CGT→CGG pyrC' → Dihydroorotase‑like protein
RA 5,688,625 A→C 32.0% S232R (AGC→CGC)  pyrC' → Dihydroorotase‑like protein
RA 5,688,634 A→C 35.3% T235P (ACC→CCC)  pyrC' → Dihydroorotase‑like protein
RA 5,688,637 A→C 71.3% S236R (AGC→CGC)  pyrC' → Dihydroorotase‑like protein
RA 5,688,645 T→G 55.5% R238R (CGT→CGG pyrC' → Dihydroorotase‑like protein
RA 5,717,363 A→C 20.6% V753G (GTG→GGG)  opgH ← Glucans biosynthesis glucosyltransferase H
RA 5,756,055 Δ1 bp 100% coding (776/834 nt) CJ019_05400 → hypothetical protein
RA 5,773,403 T→G 22.5% F334V (TTC→GTC)  nhaP2_2 → K( )/H( ) antiporter NhaP2
RA 5,917,508 G→A 6.6% G53G (GGC→GGT gcvH_2 ← Glycine cleavage system H protein
RA 5,952,038 T→C 6.0% L929P (CTG→CCG)  CJ019_05572 → hypothetical protein
RA 5,954,599 C→T 6.3% A280V (GCC→GTC)  lysA_2 → Diaminopimelate decarboxylase
RA 6,020,344 T→G 49.7% S57R (AGC→CGC)  ycaD_4 ← putative MFS‑type transporter YcaD
RA 6,144,061 C→T 6.1% A137V (GCG→GTG)  bpsA → N(4)‑bis(aminopropyl)spermidine synthase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ ACB122 80677 80860 184 21 [17] [18] 19 [gcvA_2] [gcvA_2]
* * ÷ ACB122 87938 88059 122 19 [18] [18] 20 [CJ019_00094]–[CJ019_00095] [CJ019_00094],[CJ019_00095]
* * ÷ ACB122 213570 213677 108 19 [17] [15] 19 [CJ019_00185] [CJ019_00185]
* * ÷ ACB122 517190 517304 115 24 [16] [18] 19 tyrS/birA Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA
* * ÷ ACB122 674284 674396 113 19 [18] [18] 19 [nimR_1]–[mcpH_2] [nimR_1],[mcpH_2]
* * ÷ ACB122 711481 711559 79 19 [18] [18] 19 [aam] [aam]
* * ÷ ACB122 908070 908218 149 19 [18] [15] 20 [fruA] [fruA]
* * ÷ ACB122 1119625 1119715 91 19 [18] [10] 19 tdcG_2/gcvP_1 L‑serine dehydratase TdcG/Glycine dehydrogenase (decarboxylating)
* * ÷ ACB122 1304741 1304854 114 23 [18] [15] 19 CJ019_01223/rapA putative signaling protein/RNA polymerase‑associated protein RapA
* * ÷ ACB122 1360609 1361021 413 20 [18] [17] 19 [CJ019_01275] [CJ019_01275]
* * ÷ ACB122 1376260 1376336 77 19 [17] [13] 22 CJ019_01289 hypothetical protein
* * ÷ ACB122 1396593 1396673 81 19 [17] [18] 19 [mcpU_1] [mcpU_1]
* * ÷ ACB122 1457206 1457300 95 21 [18] [18] 19 [algL]–[algX] [algL],[algX]
* * ÷ ACB122 1492461 1492581 121 20 [13] [10] 19 [CJ019_01406] [CJ019_01406]
* * ÷ ACB122 1585603 1585712 110 19 [17] [16] 19 CJ019_01493 hypothetical protein
* * ÷ ACB122 1632587 1632691 105 19 [16] [18] 21 czcR_4/CJ019_01536 Transcriptional activator protein CzcR/hypothetical protein
* * ÷ ACB122 1697643 1697782 140 19 [16] [18] 19 [CJ019_01593]–[CJ019_01594] [CJ019_01593],[CJ019_01594]
* * ÷ ACB122 1705077 1705224 148 19 [18] [18] 19 ppc/adk Phosphoenolpyruvate carboxylase/Adenylate kinase
* * ÷ ACB122 1914560 1914663 104 31 [15] [18] 19 [ppsC_1]–[CJ019_01830] [ppsC_1],[CJ019_01830]
* * ÷ ACB122 1940769 1940939 171 20 [18] [17] 19 [CJ019_01857] [CJ019_01857]
* * ÷ ACB122 2031218 2031457 240 19 [18] [18] 20 [wecB] [wecB]
* * ÷ ACB122 2092966 2093067 102 19 [16] [16] 24 rcsC_3/CJ019_01993 Sensor histidine kinase RcsC/hypothetical protein
* * ÷ ACB122 2288816 2288946 131 19 [17] [18] 19 [CJ019_02172] [CJ019_02172]
* * ÷ ACB122 2467207 2467225 19 33 [0] [16] 32 CJ019_02325/tal hypothetical protein/Transaldolase
* * ÷ ACB122 2646587 2646718 132 19 [18] [18] 19 [CJ019_02505] [CJ019_02505]
* * ÷ ACB122 2830079 2830282 204 23 [18] [18] 19 [gabD1] [gabD1]
* * ÷ ACB122 3046177 3046338 162 19 [16] [18] 19 [rcsC_5]–[degU_2] [rcsC_5],[degU_2]
* * ÷ ACB122 3069110 3069192 83 20 [18] [17] 19 [CJ019_02882] [CJ019_02882]
* * ÷ ACB122 3305711 3305811 101 21 [16] [17] 19 [CJ019_03107] [CJ019_03107]
* * ÷ ACB122 3459854 3459971 118 20 [15] [18] 22 [CJ019_03284] [CJ019_03284]
* * ÷ ACB122 3769364 3769474 111 20 [18] [17] 19 [CJ019_03581] [CJ019_03581]
* * ÷ ACB122 3784582 3784777 196 19 [18] [18] 22 [CJ019_03594]–[dmdC_4] [CJ019_03594],[dmdC_4]
* * ÷ ACB122 3944690 3944840 151 20 [17] [18] 19 CJ019_03729/CJ019_03730 hypothetical protein/hypothetical protein
* * ÷ ACB122 4163747 4163868 122 35 [15] [18] 19 katG/leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
* * ÷ ACB122 4331609 4331749 141 19 [17] [16] 19 [ribBA_2] [ribBA_2]
* * ÷ ACB122 4521600 4521692 93 19 [18] [18] 19 [CJ019_04289] [CJ019_04289]
* * ÷ ACB122 4666850 4667023 174 19 [17] [18] 19 [btuB_4]–[chrR] [btuB_4],[chrR]
* * ÷ ACB122 4846357 4846533 177 21 [18] [18] 19 recR/ybaB Recombination protein RecR/Nucleoid‑associated protein YbaB
* * ÷ ACB122 4944860 4945021 162 19 [17] [18] 19 [CJ019_04642] [CJ019_04642]
* * ÷ ACB122 5188787 5188898 112 19 [15] [18] 19 [CJ019_04882]–[pxpC_2] [CJ019_04882],[pxpC_2]
* * ÷ ACB122 5193555 5193691 137 26 [18] [17] 20 [gltR_4]–[CJ019_04888] [gltR_4],[CJ019_04888]
* * ÷ ACB122 5250776 5250877 102 19 [17] [18] 22 [CJ019_04947]–[CJ019_04948] [CJ019_04947],[CJ019_04948]
* * ÷ ACB122 5431894 5432024 131 19 [18] [18] 19 [rluE]–[amn] [rluE],[amn]
* * ÷ ACB122 5548210 5548322 113 20 [18] [18] 22 CJ019_05226/CJ019_05227 hypothetical protein/hypothetical protein
* * ÷ ACB122 5550445 5550609 165 22 [18] [18] 24 CJ019_05227/purA hypothetical protein/Adenylosuccinate synthetase
* * ÷ ACB122 5645609 5645681 73 19 [15] [16] 19 CJ019_05302/CJ019_05303 hypothetical protein/hypothetical protein
* * ÷ ACB122 5890344 5890489 146 19 [18] [17] 19 CJ019_05517/czcA_3 hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA
* * ÷ ACB122 5895772 5895859 88 19 [18] [18] 23 [CJ019_05521] [CJ019_05521]
* * ÷ ACB122 6073599 6073696 98 20 [18] [18] 19 [yeaD_2]–[CJ019_05690] [yeaD_2],[CJ019_05690]