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 | 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 | = 2172434 | 148 (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 | = 2930727 | 0 (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 | = 3376605 | 46 (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 | = 3376605 | 46 (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 | |||||