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 | annotation | gene | description |
| RA | 44,301 | (T)9→8 | intergenic (+132/‑359) | oprD_1 → / → czcR_2 | Porin D/Transcriptional activator protein CzcR |
| RA | 120,983 | (T)9→8 | intergenic (+280/+92) | polA → / ← engB | DNA polymerase I/putative GTP‑binding protein EngB |
| RA | 179,484 | T→C | C316R (TGC→CGC) | CJ019_00182 → | hypothetical protein |
| RA | 253,202 | C→T | G89G (GGC→GGT) | ssuC_1 → | Putative aliphatic sulfonates transport permeaseprotein SsuC |
| RA | 445,359 | A→G | H76R (CAC→CGC) | argD_1 → | Acetylornithine aminotransferase |
| RA | 465,344 | C→T | G214D (GGC→GAC) | rpoD ← | RNA polymerase sigma factor RpoD |
| RA | 587,254 | T→C | intergenic (‑65/+45) | ompW ← / ← CJ019_00551 | Outer membrane protein W/hypothetical protein |
| RA | 757,847 | T→C | Y181C (TAC→TGC) | fliY_2 ← | L‑cystine‑binding protein FliY |
| RA | 1,227,173 | A→G | V389A (GTC→GCC) | glpK ← | Glycerol kinase |
| RA | 1,312,593 | A→G | Q255R (CAG→CGG) | aaeA_2 → | p‑hydroxybenzoic acid efflux pump subunit AaeA |
| RA | 1,346,999 | A→G | R477R (CGT→CGC) | CJ019_01261 ← | hypothetical protein |
| RA | 1,652,260 | C→T | intergenic (‑11/+12) | CJ019_01548 ← / ← nudC_1 | hypothetical protein/NADH pyrophosphatase |
| RA | 1,669,326 | A→G | S25G (AGC→GGC) | thrC_2 → | Threonine synthase |
| RA | 1,735,045 | T→C | intergenic (‑77/+7) | CJ019_01633 ← / ← CJ019_01634 | hypothetical protein/hypothetical protein |
| RA | 2,020,873 | (C)7→8 | coding (606/1005 nt) | tagO → | putative undecaprenyl‑phosphateN‑acetylglucosaminyl 1‑phosphate transferase |
| RA | 2,031,417 | (G)10→9 | coding (1120/1143 nt) | wecB ← | UDP‑N‑acetylglucosamine 2‑epimerase |
| RA | 2,092,484 | A→G | Y155H (TAC→CAC) | rcsC_3 ← | Sensor histidine kinase RcsC |
| JC | 2,191,046 | +CTGAAAATATCTCTTAT | intergenic (‑1/‑313) | PP_RS10045 ← / → purU_3 | LysR family transcriptional regulator/Formyltetrahydrofolate deformylase |
| RA | 2,240,159 | A→G | F827S (TTT→TCT) | CJ019_02129 ← | hypothetical protein |
| RA | 2,281,980 | A→G | K408R (AAG→AGG) | pepN → | Aminopeptidase N |
| RA | 2,433,832 | A→G | intergenic (+30/‑71) | CJ019_02296 → / → topA | hypothetical protein/DNA topoisomerase 1 |
| RA | 3,130,824 | (T)9→8 | intergenic (+212/‑78) | livF_3 → / → oprD_7 | High‑affinity branched‑chain amino acidtransport ATP‑binding protein LivF/Porin D |
| RA | 3,181,018 | G→A | A532T (GCC→ACC) | actP_2 → | Cation/acetate symporter ActP |
| RA | 3,440,326 | A→C | S18R (AGC→CGC) | CJ019_03266 → | hypothetical protein |
| RA | 3,541,597 | (G)6→7 | coding (80/195 nt) | CJ019_03358 → | hypothetical protein |
| RA | 3,804,739 | (C)6→7 | coding (23/1185 nt) | ydhP_3 → | Inner membrane transport protein YdhP |
| RA | 3,833,928 | G→A | R406R (CGC→CGT) | nicP_8 ← | Porin‑like protein NicP |
| RA | 3,994,687 | C→T | S247S (AGC→AGT) | dmoA_3 → | Dimethyl‑sulfide monooxygenase |
| RA | 4,053,106 | A→G | L474P (CTG→CCG) | pgm ← | Phosphoglucomutase |
| RA | 4,190,676 | G→A | intergenic (+890/+101) | CJ019_03940 → / ← CJ019_03941 | hypothetical protein/hypothetical protein |
| JC | 4,257,335 | +GCGGCCGC | intergenic (‑281/+7) | CJ019_03991 ← / ← CJ019_03994 | putative ABC transporter ATP‑binding protein/hypothetical protein |
| RA | 4,428,638 | C→T | S62S (AGC→AGT) | CJ019_04204 → | hypothetical protein |
| RA | 4,437,644 | C→T | D125N (GAC→AAC) | nicD ← | N‑formylmaleamate deformylase |
| RA | 4,563,812 | C→T | S693S (AGC→AGT) | CJ019_04322 → | hypothetical protein |
| RA | 4,575,178 | (G)11→10 | intergenic (‑154/+17) | CJ019_04328 ← / ← glgE2 | Glucosamine kinase/Alpha‑1,4‑glucan:maltose‑1‑phosphatemaltosyltran s ferase 2 |
| RA | 4,713,495 | Δ2 bp | coding (1667‑1668/1905 nt) | htpG ← | Chaperone protein HtpG |
| RA | 4,749,727 | C→T | S441S (AGC→AGT) | ttgI_4 → | Toluene efflux pump outer membrane protein TtgI |
| RA | 4,759,509 | G→A | intergenic (+124/‑16) | fpvA_3 → / → ligM_KToptimized | Ferripyoverdine receptor/sequence generated by OPTIMIZER for KT2440 |
| RA | 5,009,222 | (A)11→10 | intergenic (‑166/+68) | CJ019_04705 ← / ← spuC_5 | hypothetical protein/Putrescine‑‑pyruvate aminotransferase |
| RA | 5,049,836 | (G)8→9 | coding (1335/1395 nt) | hcnB ← | Hydrogen cyanide synthase subunit HcnB |
| RA | 5,050,496 | G→A | G225G (GGC→GGT) | hcnB ← | Hydrogen cyanide synthase subunit HcnB |
| RA | 5,345,605 | G→A | Q611* (CAG→TAG) | pnp ← | Polyribonucleotide nucleotidyltransferase |
| RA | 5,386,500 | C→A | intergenic (‑509/+1142) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,503 | C→G | intergenic (‑512/+1139) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,506 | 1 bp→GT | intergenic (‑515/+1136) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,507 | +C | intergenic (‑516/+1135) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,510 | 2 bp→TA | intergenic (‑519/+1131) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,513 | +AA | intergenic (‑522/+1129) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,514 | T→C | intergenic (‑523/+1128) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,517 | G→C | intergenic (‑526/+1125) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,519 | G→A | intergenic (‑528/+1123) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,811 | C→T | intergenic (‑820/+831) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| MC JC | 5,390,395 | (CGCAT)2→1 | coding (489‑493/1666 nt) | ligH → | 10‑formyltetrahydrofolate synthetase |
| RA | 5,394,361 | (G)6→7 | coding (188/1731 nt) | CJ019_05073 → | hypothetical protein |
| RA | 5,515,237 | C→T | G157S (GGC→AGC) | CJ019_05187 ← | hypothetical protein |
| RA | 5,620,966 | A→G | Y285H (TAT→CAT) | CJ019_05282 ← | hypothetical protein |
| RA | 5,727,032 | C→T | R176R (AGG→AGA) | pip ← | Proline iminopeptidase |
| RA | 5,760,598 | (A)6→5 | coding (781/834 nt) | CJ019_05400 → | hypothetical protein |
| RA | 5,983,547 | A→G | Y207C (TAC→TGC) | cdhR_8 → | HTH‑type transcriptional regulator CdhR |
| RA | 6,137,970 | T→C | V171A (GTG→GCG) | cusA → | Cation efflux system protein CusA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | ACB143 | 82197 | 82282 | 86 | 15 [14] | [14] 15 | trpA | Tryptophan synthase alpha chain |
| * | * | ÷ | ACB143 | 161232 | 161376–161315 | 84–145 | 15 [6] | [11] 15 | [uctC_1] | [uctC_1] |
| * | * | ÷ | ACB143 | 492238 | 492319 | 82 | 15 [13] | [14] 15 | uvrY/potA_1 | Response regulator UvrY/Spermidine/putrescine import ATP‑binding proteinPotA |
| * | * | ÷ | ACB143 | 517190 | 517352 | 163 | 33 [13] | [13] 15 | tyrS/birA | Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA |
| * | * | ÷ | ACB143 | 674254 | 674389 | 136 | 15 [14] | [14] 15 | [nimR_1]–[mcpH_2] | [nimR_1],[mcpH_2] |
| * | * | ÷ | ACB143 | 1376295 | 1376324 | 30 | 15 [14] | [14] 15 | CJ019_01289 | hypothetical protein |
| * | * | ÷ | ACB143 | 1396593 | 1396679 | 87 | 16 [14] | [11] 16 | [mcpU_1] | [mcpU_1] |
| * | * | ÷ | ACB143 | 1422677–1423227 | 1424405–1423231 | 5–1729 | 15 [14] | [13] 16 | [CJ019_01343]–[CJ019_01346] | [CJ019_01343],[CJ019_01346] |
| * | * | ÷ | ACB143 | 1585608 | 1585721 | 114 | 15 [14] | [14] 16 | CJ019_01493 | hypothetical protein |
| * | * | ÷ | ACB143 | 1914563 | 1914638 | 76 | 15 [14] | [14] 15 | [ppsC_1] | [ppsC_1] |
| * | * | ÷ | ACB143 | 1923415 | 1923505 | 91 | 15 [12] | [14] 22 | [apeB] | [apeB] |
| * | * | ÷ | ACB143 | 2234293 | 2234392 | 100 | 15 [14] | [14] 17 | [gltX] | [gltX] |
| * | * | ÷ | ACB143 | 2288848 | 2288922 | 75 | 16 [14] | [12] 15 | CJ019_02171/CJ019_02172 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 2661050 | 2661159 | 110 | 15 [14] | [14] 15 | prpF/mmgE | 2‑methyl‑aconitate isomerase/Citrate/2‑methylcitrate dehydratase |
| * | * | ÷ | ACB143 | 3046177 | 3046327 | 151 | 15 [12] | [14] 15 | [rcsC_5]–[degU_2] | [rcsC_5],[degU_2] |
| * | * | ÷ | ACB143 | 3280235 | 3280341 | 107 | 15 [13] | [13] 15 | [CJ019_03085]–[xthA_2] | [CJ019_03085],[xthA_2] |
| * | * | ÷ | ACB143 | 3769390 | 3769462 | 73 | 16 [14] | [14] 15 | CJ019_03581/CJ019_03582 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 4344757 | 4344813 | 57 | 15 [11] | [14] 15 | nmoA | Nitronate monooxygenase |
| * | * | ÷ | ACB143 | 4521592 | 4521679 | 88 | 16 [10] | [13] 15 | CJ019_04289/topB | Acetyltransferase/DNA topoisomerase 3 |
| * | * | ÷ | ACB143 | 4732395 | 4732465 | 71 | 15 [14] | [12] 18 | gltA/CJ019_04468 | Citrate synthase/hypothetical protein |
| * | * | ÷ | ACB143 | 4845672 | 4845852 | 181 | 16 [13] | [8] 15 | recR/ybaB | Recombination protein RecR/Nucleoid‑associated protein YbaB |
| * | * | ÷ | ACB143 | 4944238 | 4944345 | 108 | 15 [14] | [14] 16 | [CJ019_04642] | [CJ019_04642] |
| * | * | ÷ | ACB143 | 5192938 | 5193023 | 86 | 15 [12] | [14] 15 | [gltR_4]–[CJ019_04888] | [gltR_4],[CJ019_04888] |
| * | * | ÷ | ACB143 | 5250131 | 5250222 | 92 | 16 [14] | [13] 18 | [CJ019_04947]–[CJ019_04948] | [CJ019_04947],[CJ019_04948] |
| * | * | ÷ | ACB143 | 5482252 | 5482403 | 152 | 16 [14] | [13] 15 | [purH] | [purH] |
| * | * | ÷ | ACB143 | 5503643 | 5503836 | 194 | 15 [14] | [14] 15 | [CJ019_05176] | [CJ019_05176] |
| * | * | ÷ | ACB143 | 5900314 | 5900394 | 81 | 16 [14] | [14] 18 | [CJ019_05521] | [CJ019_05521] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | ACB143 | 1290801 = | NA (NA) | 46 (0.770) | 24/258 | 0.9 | NA | coding (936/1329 nt) | CJ019_01212 | IS110 family transposase ISPpu9 |
| ? | ACB143 | = 1291580 | NA (NA) | intergenic (+386/+43) | CJ019_01212/CJ019_01213 | IS110 family transposase ISPpu9/hypothetical protein | |||||
| * | ? | ACB143 | 1837190 = | 0 (0.000) | 56 (0.960) | 31/252 | 0.4 | 55.5% | coding (660/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | = 2172433 | 90 (1.550) | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein | |||||
| * | ? | ACB143 | = 1837193 | 0 (0.000) | 27 (0.460) | 19/254 | 1.3 | 42.9% | coding (657/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | 2170759 = | 72 (1.230) | intergenic (‑774/‑63) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 | |||||
| * | ? | ACB143 | 2155685 = | 81 (1.340) | 56 (0.930) | 29/262 | 0.6 | 46.9% | coding (301/369 nt) | tmk_1 | Thymidylate kinase |
| ? | ACB143 | = 2220562 | 46 (0.760) | coding (36/369 nt) | tmk_2 | Thymidylate kinase | |||||
| * | ? | ACB143 | 2170758 = | 72 (1.190) | 41 (0.690) | 28/258 | 0.6 | 53.3% | intergenic (‑773/‑64) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 5563630 = | 1 (0.020) | coding (1047/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | = 2172434 | 91 (1.510) | 48 (0.800) | 30/260 | 0.5 | 51.2% | intergenic (+176/+92) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 5563631 | 1 (0.020) | coding (1046/1902 nt) | mutL_2 | DNA mismatch repair protein MutL | |||||
| * | ? | ACB143 | = 2930727 | 0 (0.000) | 64 (1.080) | 24/258 | 0.9 | 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 = | 22 (0.360) | 87 (1.440) | 53/262 | 0.0 | 88.8% | intergenic (+219/‑151) | pikAII_1/CJ019_03160 | Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42 |
| ? | ACB143 | 5775225 = | 0 (0.000) | coding (1544/2151 nt) | CJ019_05409 | hypothetical protein | |||||
| * | ? | ACB143 | = 3376605 | 81 (1.340) | 56 (0.930) | 31/260 | 0.4 | 56.7% | coding (501/546 nt) | CJ019_03184 | hypothetical protein |
| ? | ACB143 | = 5775229 | 5 (0.080) | coding (1540/2151 nt) | CJ019_05409 | hypothetical protein | |||||