mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 343,673 | T→C | 54.1% | G12G (GGT→GGC) | hisH → | Imidazole glycerol phosphate synthase subunitHisH |
| RA | 358,766 | C→T | 26.5% | intergenic (‑115/‑30) | CJ019_00331 ← / → cdhR_2 | hypothetical protein/HTH‑type transcriptional regulator CdhR |
| RA | 456,874 | T→C | 25.5% | M425V (ATG→GTG) | iaaM ← | Tryptophan 2‑monooxygenase |
| RA | 586,555 | A→C | 20.8% | V212G (GTC→GGC) | ompW ← | Outer membrane protein W |
| RA | 841,643 | G→T | 22.5% | H609N (CAT→AAT) | CJ019_00805 ← | hypothetical protein |
| RA | 844,922 | C→T | 6.2% | A217A (GCC→GCT) | hemA → | Glutamyl‑tRNA reductase |
| RA | 910,666 | A→G | 38.5% | intergenic (‑50/+149) | CJ019_00872 ← / ← oprD_4 | hypothetical protein/Porin D |
| RA | 924,333 | T→G | 12.2% | D4780A (GAC→GCC) | CJ019_00881 ← | hypothetical protein |
| RA | 1,113,257 | C→T | 7.6% | L18L (CTG→CTA) | pepA ← | Cytosol aminopeptidase |
| RA | 1,630,540 | A→C | 20.6% | L419R (CTG→CGG) | czcS ← | Sensor protein CzcS |
| RA | 1,643,529 | C→T | 10.0% | S196N (AGC→AAC) | CJ019_01543 ← | putative TonB‑dependent receptor |
| RA | 1,754,756 | A→G | 29.3% | K287R (AAG→AGG) | CJ019_01665 → | hypothetical protein |
| JC | 2,142,770 | (TCGATCTGGCTT)1→2 | 81.2% | coding (807/3276 nt) | rne ← | Ribonuclease E |
| RA | 2,175,073 | A→G | 6.5% | intergenic (‑8/‑174) | CJ019_02064 ← / → CJ019_02065 | hypothetical protein/hypothetical protein |
| JC | 2,191,046 | +CTGAAAATATCTCTTAT | 100% | intergenic (‑1/‑313) | PP_RS10045 ← / → purU_3 | LysR family transcriptional regulator/Formyltetrahydrofolate deformylase |
| RA | 2,390,993 | T→G | 30.3% | E566D (GAA→GAC) | bvgS ← | Virulence sensor protein BvgS |
| RA | 2,598,770 | C→T | 11.8% | T80T (ACC→ACT) | CJ019_02459 → | hypothetical protein |
| RA | 2,729,080 | T→A | 9.1% | C980S (TGC→AGC) | CJ019_02576 → | hypothetical protein |
| RA | 2,775,009 | C→T | 43.6% | A112T (GCC→ACC) | iscS_2 ← | Cysteine desulfurase IscS |
| RA | 2,779,225 | A→G | 10.8% | S162P (TCG→CCG) | alx_1 ← | Putative membrane‑bound redox modulator Alx |
| RA | 2,908,411 | A→G | 67.9% | Y1464C (TAC→TGC) | CJ019_02759 → | hypothetical protein |
| RA | 2,954,230 | A→G | 8.2% | intergenic (‑77/+41) | fatA_2 ← / ← fatB | Ferric‑anguibactin receptor FatA/Ferric‑anguibactin‑binding protein FatB |
| RA | 3,080,143 | G→A | 6.4% | G148D (GGC→GAC) | cynR_2 → | HTH‑type transcriptional regulator CynR |
| RA | 3,185,620 | G→A | 13.9% | P302L (CCG→CTG) | prr_2 ← | Gamma‑aminobutyraldehyde dehydrogenase |
| RA | 3,360,157 | C→T | 29.8% | I138I (ATC→ATT) | CJ019_03160 → | Tn3 family transposase ISPa42 |
| RA | 3,815,010 | G→A | 33.9% | A405V (GCG→GTG) | ttuB_3 ← | Putative tartrate transporter |
| RA | 4,003,911 | G→A | 28.6% | R113C (CGC→TGC) | pobA ← | p‑hydroxybenzoate hydroxylase |
| RA | 4,156,467 | C→T | 5.9% | R203H (CGT→CAT) | pssA ← | CDP‑diacylglycerol‑‑serineO‑phosphatidyltransfer a se |
| RA | 4,198,609 | G→A | 13.0% | T932I (ACC→ATC) | CJ019_03944 ← | hypothetical protein |
| RA | 4,245,128 | A→C | 32.6% | 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 | 4,624,111 | C→A | 16.4% | intergenic (+117/+181) | CJ019_04367 → / ← pgsA | hypothetical protein/CDP‑diacylglycerol‑‑glycerol‑3‑phosphate 3‑phosphatidyltransferase |
| RA | 4,640,631 | A→G | 44.5% | V30A (GTG→GCG) | bicA ← | Bicarbonate transporter BicA |
| RA | 4,645,929 | T→C | 11.4% | F270L (TTC→CTC) | aceA → | Isocitrate lyase |
| RA | 4,669,221 | C→T | 7.8% | G318R (GGG→AGG) | adiA ← | Biodegradative arginine decarboxylase |
| RA | 4,724,990 | C→A | 8.5% | L748L (CTG→CTT) | sucA ← | 2‑oxoglutarate dehydrogenase E1 component |
| RA | 4,759,606 | G→A | 100% | A28T (GCC→ACC) | ligM_KToptimized → | sequence generated by OPTIMIZER for KT2440 |
| RA | 4,916,414 | C→T | 6.7% | G54S (GGC→AGC) | cheW ← | Chemotaxis protein CheW |
| RA | 4,955,371 | G→A | 23.5% | P128L (CCG→CTG) | atoC_3 ← | Regulatory protein AtoC |
| RA | 5,095,398 | A→T | 7.4% | I66F (ATC→TTC) | phhA → | Phenylalanine‑4‑hydroxylase |
| RA | 5,096,422 | C→A | 29.0% | intergenic (+35/‑155) | CJ019_04792 → / → CJ019_04793 | Putative pterin‑4‑alpha‑carbinolaminedehydratase/hypothetical protein |
| RA | 5,107,530 | G→A | 8.2% | V25V (GTC→GTT) | scpA ← | Segregation and condensation protein A |
| RA | 5,245,005 | C→A | 29.5% | L177M (CTG→ATG) | gltC_4 → | HTH‑type transcriptional regulator GltC |
| RA | 5,327,077 | T→C | 25.1% | L63P (CTG→CCG) | sasA_18 → | Adaptive‑response sensory‑kinase SasA |
| RA | 5,328,860 | G→A | 46.3% | W657* (TGG→TGA) | sasA_18 → | Adaptive‑response sensory‑kinase SasA |
| RA | 5,334,186 | A→T | 14.6% | intergenic (+236/‑27) | folK → / → panB | 2‑amino‑4‑hydroxy‑6‑hydroxymethyldihydropteridin e pyrophosphokinase/3‑methyl‑2‑oxobutanoatehydroxymethyltransferase |
| 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 |
| RA | 5,390,208 | G→A | 28.0% | G101D (GGC→GAC) | ligH → | 10‑formyltetrahydrofolate synthetase |
| RA | 5,481,631 | G→A | 7.7% | A320A (GCG→GCA) | purH → | Bifunctional purine biosynthesis protein PurH |
| RA | 5,485,083 | C→A | 13.3% | I409I (ATC→ATA) | rcsC_18 → | Sensor histidine kinase RcsC |
| RA | 5,525,438 | G→A | 5.9% | S178S (AGC→AGT) | sdh ← | Serine 3‑dehydrogenase |
| RA | 5,593,070 | T→C | 12.9% | Y66C (TAT→TGT) | thiC ← | Phosphomethylpyrimidine synthase |
| RA | 5,644,213 | T→C | 9.1% | D188G (GAC→GGC) | CJ019_05296 ← | hypothetical protein |
| RA | 5,667,963 | C→T | 7.0% | Q91* (CAG→TAG) | CJ019_05320 → | hypothetical protein |
| RA | 5,693,153 | T→G | 34.3% | R228R (CGT→CGG) | pyrC' → | Dihydroorotase‑like protein |
| RA | 5,693,175 | A→C | 40.7% | S236R (AGC→CGC) | pyrC' → | Dihydroorotase‑like protein |
| RA | 5,760,593 | Δ1 bp | 100% | coding (776/834 nt) | CJ019_05400 → | hypothetical protein |
| RA | 5,994,584 | G→A | 20.2% | G220G (GGC→GGT) | CJ019_05610 ← | Arylesterase |
| RA | 6,120,698 | G→A | 5.6% | A35V (GCG→GTG) | gbsA ← | Betaine aldehyde dehydrogenase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | ACB143 | 161232 | 161403–161315 | 84–172 | 16 [12] | [14] 15 | [uctC_1] | [uctC_1] |
| * | * | ÷ | ACB143 | 517193 | 517314 | 122 | 15 [13] | [14] 15 | tyrS/birA | Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA |
| * | * | ÷ | ACB143 | 607303 | 607407 | 105 | 16 [14] | [14] 15 | dxs/ispA | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase/Farnesyl diphosphate synthase |
| * | * | ÷ | ACB143 | 674256 | 674384 | 129 | 15 [13] | [12] 15 | [nimR_1]–[mcpH_2] | [nimR_1],[mcpH_2] |
| * | * | ÷ | ACB143 | 1304774 | 1304842 | 69 | 15 [14] | [14] 15 | CJ019_01223/rapA | putative signaling protein/RNA polymerase‑associated protein RapA |
| * | * | ÷ | ACB143 | 1376267 | 1376337 | 71 | 16 [14] | [14] 16 | CJ019_01289 | hypothetical protein |
| * | * | ÷ | ACB143 | 1499912 | 1500058 | 147 | 17 [13] | [14] 17 | [petC]–[sspA] | [petC],[sspA] |
| * | * | ÷ | ACB143 | 1585604 | 1585706 | 103 | 15 [14] | [14] 15 | CJ019_01493 | hypothetical protein |
| * | * | ÷ | ACB143 | 1632579 | 1632684 | 106 | 17 [14] | [14] 21 | czcR_4/CJ019_01536 | Transcriptional activator protein CzcR/hypothetical protein |
| * | * | ÷ | ACB143 | 1914546 | 1914680 | 135 | 16 [14] | [13] 15 | [ppsC_1]–[CJ019_01830] | [ppsC_1],[CJ019_01830] |
| * | * | ÷ | ACB143 | 1923378 | 1923542 | 165 | 15 [13] | [14] 15 | [apeB] | [apeB] |
| * | * | ÷ | ACB143 | 1940792 | 1940933 | 142 | 15 [13] | [12] 15 | [CJ019_01857] | [CJ019_01857] |
| * | * | ÷ | ACB143 | 2234306 | 2234409 | 104 | 15 [14] | [14] 15 | gltX/PP_RS08750 | Glutamate‑‑tRNA ligase/tRNA‑Val |
| * | * | ÷ | ACB143 | 2288847 | 2288951 | 105 | 15 [14] | [14] 15 | [CJ019_02172] | [CJ019_02172] |
| * | * | ÷ | ACB143 | 2467190 | 2467208 | 19 | 22 [0] | [9] 36 | CJ019_02325/tal | hypothetical protein/Transaldolase |
| * | * | ÷ | ACB143 | 3046187 | 3046330 | 144 | 15 [14] | [12] 16 | [rcsC_5]–[degU_2] | [rcsC_5],[degU_2] |
| * | * | ÷ | ACB143 | 3839283 | 3839392 | 110 | 17 [14] | [14] 15 | [argP_2] | [argP_2] |
| * | * | ÷ | ACB143 | 3944649 | 3944782 | 134 | 15 [14] | [14] 16 | [CJ019_03729] | [CJ019_03729] |
| * | * | ÷ | ACB143 | 4163761 | 4163876 | 116 | 17 [12] | [14] 18 | katG/leuO_2 | Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO |
| * | * | ÷ | ACB143 | 4331629 | 4331732 | 104 | 15 [14] | [11] 15 | ribBA_2/potD_2 | Riboflavin biosynthesis protein RibBA/Spermidine/putrescine‑binding periplasmicprotein |
| * | * | ÷ | ACB143 | 4344727 | 4344818 | 92 | 15 [14] | [14] 15 | nmoA | Nitronate monooxygenase |
| * | * | ÷ | ACB143 | 4521586 | 4521682 | 97 | 15 [13] | [14] 15 | [CJ019_04289] | [CJ019_04289] |
| * | * | ÷ | ACB143 | 4666863 | 4666983 | 121 | 15 [14] | [14] 15 | [btuB_4] | [btuB_4] |
| * | * | ÷ | ACB143 | 4732397 | 4732515 | 119 | 15 [14] | [14] 15 | [CJ019_04468] | [CJ019_04468] |
| * | * | ÷ | ACB143 | 4845670 | 4845852 | 183 | 17 [14] | [13] 16 | recR/ybaB | Recombination protein RecR/Nucleoid‑associated protein YbaB |
| * | * | ÷ | ACB143 | 4944212 | 4944339 | 128 | 15 [14] | [12] 15 | [CJ019_04642] | [CJ019_04642] |
| * | * | ÷ | ACB143 | 5192928 | 5193044 | 117 | 16 [12] | [13] 16 | [gltR_4]–[CJ019_04888] | [gltR_4],[CJ019_04888] |
| * | * | ÷ | ACB143 | 5250116 | 5250222 | 107 | 15 [14] | [13] 15 | [CJ019_04947]–[CJ019_04948] | [CJ019_04947],[CJ019_04948] |
| * | * | ÷ | ACB143 | 5474276 | 5474410 | 135 | 15 [14] | [14] 15 | [CJ019_05148] | [CJ019_05148] |
| * | * | ÷ | ACB143 | 5503652 | 5503820 | 169 | 15 [14] | [14] 15 | [CJ019_05176] | [CJ019_05176] |
| * | * | ÷ | ACB143 | 5678556 | 5678651 | 96 | 15 [13] | [13] 15 | CJ019_05328/CJ019_05329 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 5894914 | 5895007 | 94 | 17 [12] | [14] 15 | CJ019_05517/czcA_3 | hypothetical protein/Cobalt‑zinc‑cadmium resistance protein CzcA |
| * | * | ÷ | ACB143 | 5900298 | 5900397 | 100 | 16 [14] | [12] 15 | [CJ019_05521] | [CJ019_05521] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | ACB143 | 1837190 = | 1 (0.020) | 48 (1.060) | 26/232 | NT | 48.7% | coding (660/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | = 2172433 | 100 (2.200) | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein | |||||
| * | ? | ACB143 | = 1837193 | 1 (0.020) | 22 (0.480) | 18/234 | NT | 41.5% | coding (657/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | 2170759 = | 61 (1.330) | intergenic (‑774/‑63) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 | |||||
| * | ? | ACB143 | 2155685 = | 56 (1.180) | 67 (1.410) | 37/242 | NT | 57.3% | coding (301/369 nt) | tmk_1 | Thymidylate kinase |
| ? | ACB143 | = 2220562 | 44 (0.930) | coding (36/369 nt) | tmk_2 | Thymidylate kinase | |||||
| * | ? | ACB143 | 2170755 = | 61 (1.290) | 8 (0.170) | 5/234 | NT | 14.5% | intergenic (‑770/‑67) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 2716447 = | 35 (0.760) | coding (185/846 nt) | rhaR_3 | HTH‑type transcriptional activator RhaR | |||||
| * | ? | ACB143 | 2170758 = | 64 (1.350) | 23 (0.490) | 19/240 | NT | 36.1% | intergenic (‑773/‑64) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | = 5563631 | 18 (0.380) | coding (1046/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | 2170758 = | 64 (1.350) | 7 (0.150) | 5/240 | NT | 10.6% | intergenic (‑773/‑64) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 5869157 = | 55 (1.170) | coding (690/2280 nt) | ptsP | Phosphoenolpyruvate‑dependent phosphotransferasesystem | |||||
| * | ? | ACB143 | = 2172433 | 103 (2.170) | 5 (0.110) | 5/242 | NT | 6.0% | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 5869159 | 55 (1.160) | coding (688/2280 nt) | ptsP | Phosphoenolpyruvate‑dependent phosphotransferasesystem | |||||
| * | ? | ACB143 | = 2172434 | 101 (2.130) | 40 (0.860) | 26/238 | NT | 40.5% | intergenic (+176/+92) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | 5563630 = | 18 (0.390) | coding (1047/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | = 2172438 | 100 (2.110) | 5 (0.110) | 5/232 | NT | 7.1% | intergenic (+180/+88) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 2716441 | 35 (0.770) | coding (191/846 nt) | rhaR_3 | HTH‑type transcriptional activator RhaR | |||||
| * | ? | ACB143 | 3359593 = | 38 (0.800) | 15 (0.320) | 10/242 | NT | 28.8% | intergenic (+219/‑151) | pikAII_1/CJ019_03160 | Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42 |
| ? | ACB143 | 4755885 = | 36 (0.760) | coding (684/1659 nt) | yojI | ABC transporter ATP‑binding/permease proteinYojI | |||||
| * | ? | ACB143 | = 3376605 | 53 (1.120) | 25 (0.530) | 20/242 | NT | 29.8% | coding (501/546 nt) | CJ019_03184 | hypothetical protein |
| ? | ACB143 | = 4765778 | 65 (1.370) | coding (6629/10413 nt) | grsB | Gramicidin S synthase 2 | |||||