mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.0 revision fe39cd8f5880
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NODE_2 | 134,755 | G→A | intergenic (+202/‑293) | aqpZ → / → lysO | aquaporin Z/L‑lysine exporter LysO |
| RA | NODE_20 | 45,821 | Δ2 bp | intergenic (+2/‑2) | EcoliAnna_02842 → / → EcoliAnna_02843 | tRNA‑Val/tRNA‑Lys |
| RA | NODE_20 | 46,127 | Δ1 bp | intergenic (+3/‑2) | EcoliAnna_02844 → / → EcoliAnna_02845 | tRNA‑Val/tRNA‑Lys |
| RA | NODE_39 | 4,254 | G→T | L210L (CTG→CTT) | EcoliAnna_03722 → | IS5‑like element ISKpn26 family transposase |
| RA | NODE_4 | 17,237 | A→G | intergenic (+1023/+707) | chaA → / ← kdsA | sodium‑potassium/proton antiporter ChaA/3‑deoxy‑8‑phosphooctulonate synthase |
| RA | NODE_4 | 17,601 | A→C | intergenic (+1387/+343) | chaA → / ← kdsA | sodium‑potassium/proton antiporter ChaA/3‑deoxy‑8‑phosphooctulonate synthase |
| RA | NODE_4 | 17,634 | Δ1 bp | intergenic (+1420/+310) | chaA → / ← kdsA | sodium‑potassium/proton antiporter ChaA/3‑deoxy‑8‑phosphooctulonate synthase |
| RA | NODE_4 | 17,639 | +A | intergenic (+1425/+305) | chaA → / ← kdsA | sodium‑potassium/proton antiporter ChaA/3‑deoxy‑8‑phosphooctulonate synthase |
| RA | NODE_4 | 17,642 | C→A | intergenic (+1428/+302) | chaA → / ← kdsA | sodium‑potassium/proton antiporter ChaA/3‑deoxy‑8‑phosphooctulonate synthase |
| RA | NODE_97 | 18 | T→C | intergenic (–/–) | – / – | –/– |
| RA | NODE_97 | 65 | T→G | intergenic (–/–) | – / – | –/– |
| RA | NODE_97 | 98 | G→A | intergenic (–/–) | – / – | –/– |
| RA | NODE_97 | 104 | C→T | intergenic (–/–) | – / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NODE_29 | 46294 | 46324 | 31 | 207 [198] | [0] NA | rpsT/– | 30S ribosomal protein S20/– |
| * | * | ÷ | NODE_34 | 1 | 46 | 46 | NA [0] | [2] 262 | –/dppA | –/dipeptide ABC transporter substrate‑binding protein DppA |
| * | * | ÷ | NODE_49 | 1 | 110 | 110 | NA [0] | [227] 230 | –/tldD_2 | –/metalloprotease TldD |
| * | * | ÷ | NODE_52 | 1 | 55 | 55 | NA [0] | [0] 272 | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR |
| * | * | ÷ | NODE_57 | 12827 | 12883 | 57 | 269 [1] | [0] NA | argE/– | acetylornithine deacetylase/– |
| * | * | ÷ | NODE_94 | 1 | 8 | 8 | NA [0] | [0] 1203 | –/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NODE_13 | = 114251 | 0 (0.000) | 103 (0.100) | 70/184 | 1.3 | 100% | intergenic (‑92/–) | ypjA_2/– | adhesin‑like autotransporter YpjA/EhaD/– |
| ? | NODE_83 | = 1067 | 0 (0.000) | intergenic (+72/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_14 | = 77 | NA (NA) | 259 (1.200) +46 bp |
116/206 | 0.3 | 100% | intergenic (–/‑68) | –/EcoliAnna_02239 | –/hypothetical protein |
| ? | NODE_35 | 1 = | 0 (0.000) | noncoding (1/76 nt) | EcoliAnna_03558 | tRNA‑Asp | |||||
| * | ? | NODE_17 | = 104175 | 0 (0.000) | 204 (0.190) | 108/178 | 0.3 | 100% | intergenic (+157/–) | EcoliAnna_02650/– | tRNA‑Leu/– |
| ? | NODE_83 | = 1064 | 0 (0.000) | intergenic (+69/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_18 | = 28791 | 319 (1.180) | 229 (0.860) | 154/298 | 0.4 | 41.8% | coding (1102/1410 nt) | EcoliAnna_02682 | hypothetical protein |
| ? | NODE_66 | 4091 = | NA (NA) | coding (14/363 nt) | EcoliAnna_04262 | hypothetical protein | |||||
| * | ? | NODE_18 | 86488 = | NA (NA) | 162 (0.990) +60 bp |
70/178 | 2.7 | NA | intergenic (‑280/+1) | yqaB/EcoliAnna_02742 | fructose‑1‑phosphate/6‑phosphogluconate phosphatase/tRNA‑Arg |
| ? | NODE_6 | = 77 | NA (NA) | intergenic (‑1/+3) | EcoliAnna_01179/EcoliAnna_01180 | tRNA‑Arg/tRNA‑Ser | |||||
| * | ? | NODE_19 | 1 = | 0 (0.000) | 121 (0.080) | 80/262 | 2.9 | 100% | intergenic (–/+44) | –/wbbL_1 | –/Rhamnosyltransferase WbbL |
| ? | NODE_83 | 19 = | 0 (0.000) | coding (5/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_19 | = 15666 | 117 (0.570) | 15 (0.680) +133 bp |
11/32 | 0.8 | 55.3% | intergenic (‑133/+143) | wcaK/wzxC | colanic acid biosynthesis pyruvyl transferase WcaK/M‑antigen undecaprenyl disphosphate flippase |
| ? | NODE_19 | 15708 = | 109 (0.530) | intergenic (‑175/+101) | wcaK/wzxC | colanic acid biosynthesis pyruvyl transferase WcaK/M‑antigen undecaprenyl disphosphate flippase | |||||
| * | ? | NODE_2 | 1 = | 0 (0.000) | 558 (0.560) | 185/298 | 0.0 | 100% | intergenic (–/‑160) | –/EcoliAnna_00414 | –/threonine‑rich inner membrane protein GfcA |
| ? | NODE_94 | = 576 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_2 | 2 = | 2 (0.010) | 618 (0.630) +C |
133/296 | 0.5 | 99.8% | intergenic (–/‑159) | –/EcoliAnna_00414 | –/threonine‑rich inner membrane protein GfcA |
| ? | NODE_94 | = 576 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_21 | = 66680 | 0 (0.000) | 110 (0.100) | 75/178 | 1.3 | 100% | intergenic (‑88/–) | ybeQ/– | Sel1 family TPR‑like repeat protein YbeQ/– |
| ? | NODE_83 | = 1064 | 0 (0.000) | intergenic (+69/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_24 | 1 = | 0 (0.000) | 155 (0.730) | 95/184 | 1.8 | 100% | intergenic (–/‑451) | –/EcoliAnna_03042 | –/phosphoenolpyruvate carboxylase |
| ? | NODE_57 | = 12826 | 0 (0.000) | intergenic (+146/–) | argE/– | acetylornithine deacetylase/– | |||||
| * | ? | NODE_25 | = 58798 | 0 (0.000) | 786 (0.680) | 155/186 | 0.0 | 100% | intergenic (+35/–) | pldA/– | phospholipase A/– |
| ? | NODE_83 | = 1068 | 0 (0.000) | intergenic (+73/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_26 | = 57838 | 0 (0.000) | 166 (0.150) | 86/186 | 2.0 | 100% | intergenic (+73/–) | EcoliAnna_03216/– | oligosaccharide flippase family protein/– |
| ? | NODE_83 | = 1068 | 0 (0.000) | intergenic (+73/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_27 | = 54089 | 0 (0.000) | 171 (0.680) | 104/206 | 2.3 | 100% | intergenic (+226/–) | EcoliAnna_03267/– | tRNA‑Pro/– |
| ? | NODE_34 | 47 = | 0 (0.000) | intergenic (–/‑684) | –/dppA | –/dipeptide ABC transporter substrate‑binding protein DppA | |||||
| * | ? | NODE_30 | 1 = | 0 (0.000) | 108 (0.100) | 71/184 | 2.2 | 100% | intergenic (–/‑148) | –/EcoliAnna_03357 | –/hypothetical protein |
| ? | NODE_83 | = 1067 | 0 (0.000) | intergenic (+72/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_32 | = 41346 | 0 (0.000) | 185 (1.070) | 109/188 | 0.1 | 100% | intergenic (+298/–) | codA/– | Cytosine deaminase/– |
| ? | NODE_52 | 56 = | 0 (0.000) | intergenic (–/+38) | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR | |||||
| * | ? | NODE_36 | = 15379 | 219 (0.860) | 26 (0.800) +130 bp |
14/38 | 1.3 | 47.1% | intergenic (+58/+137) | purK/EcoliAnna_03628 | 5‑(carboxyamino)imidazole ribonucleotide synthase/carbamate kinase |
| ? | NODE_36 | 15414 = | 238 (0.930) | intergenic (+93/+102) | purK/EcoliAnna_03628 | 5‑(carboxyamino)imidazole ribonucleotide synthase/carbamate kinase | |||||
| * | ? | NODE_38 | 1 = | 0 (0.000) | 1092 (1.100) | 230/282 | 0.0 | 100% | intergenic (–/‑281) | –/EcoliAnna_03684 | –/hypothetical protein |
| ? | NODE_94 | 9 = | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_39 | = 35183 | 0 (0.000) | 102 (0.090) | 67/190 | 1.2 | 100% | intergenic (‑197/–) | EcoliAnna_03758/– | hypothetical protein/– |
| ? | NODE_83 | = 1070 | 0 (0.000) | intergenic (+75/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_4 | = 189380 | 0 (0.000) | 204 (0.970) +AT |
122/294 | 0.5 | 100% | intergenic (‑303/–) | ghrA/– | glyoxylate/hydroxypyruvate reductase GhrA/– |
| ? | NODE_76 | = 1792 | 0 (0.000) | intergenic (+389/–) | EcoliAnna_04287/– | hypothetical protein/– | |||||
| * | ? | NODE_40 | 33918 = | NA (NA) | 106 (0.640) +55 bp |
63/188 | 1.9 | NA | intergenic (‑462/–) | EcoliAnna_03789/– | IS3‑like element IS3 family transposase/– |
| ? | NODE_44 | 31549 = | NA (NA) | intergenic (‑230/–) | EcoliAnna_03915/– | GTPase family protein/– | |||||
| * | ? | NODE_44 | 1 = | 0 (0.000) | 103 (0.090) | 69/190 | 1.4 | 100% | intergenic (–/‑142) | –/wbbL_2 | –/Rhamnosyltransferase WbbL |
| ? | NODE_83 | = 1070 | 0 (0.000) | intergenic (+75/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_45 | = 31140 | 0 (0.000) | 133 (0.620) | 91/196 | 2.4 | 100% | intergenic (+262/–) | EcoliAnna_03942/– | AsmA2 domain‑containing protein/– |
| ? | NODE_49 | 52 = | 0 (0.000) | intergenic (–/‑167) | –/tldD_2 | –/metalloprotease TldD | |||||
| * | ? | NODE_48 | 1 = | 0 (0.000) | 209 (0.180) | 108/190 | 1.0 | 100% | intergenic (–/+33) | –/EcoliAnna_03993 | –/hypothetical protein |
| ? | NODE_83 | = 1070 | 0 (0.000) | intergenic (+75/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_5 | = 162437 | 275 (0.870) | 31 (0.860) +132 bp |
17/34 | 0.8 | 48.5% | intergenic (+97/+84) | EcoliAnna_01167/cca | undecaprenyl‑diphosphate phosphatase/fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase Cca |
| ? | NODE_5 | 162477 = | 301 (0.960) | intergenic (+137/+44) | EcoliAnna_01167/cca | undecaprenyl‑diphosphate phosphatase/fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase Cca | |||||
| * | ? | NODE_53 | = 108 | 394 (0.900) | 23 (0.610) +136 bp |
15/26 | 0.9 | 38.5% | intergenic (–/+165) | –/EcoliAnna_04105 | –/NAD(P)H‑flavin reductase |
| ? | NODE_53 | 152 = | 450 (1.030) | intergenic (–/+121) | –/EcoliAnna_04105 | –/NAD(P)H‑flavin reductase | |||||
| * | ? | NODE_53 | = 21980 | 0 (0.000) | 1509 (0.930) | 217/260 | 0.0 | 100% | intergenic (‑337/–) | recQ/– | ATP‑dependent DNA helicase RecQ/– |
| ? | NODE_83 | 20 = | 0 (0.000) | coding (6/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_55 | = 14553 | 0 (0.000) | 136 (0.090) | 82/252 | 2.3 | 100% | intergenic (‑463/–) | narP/– | nitrate/nitrite response regulator protein NarP/– |
| ? | NODE_83 | 24 = | 0 (0.000) | coding (10/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_62 | 1 = | 0 (0.000) | 155 (0.100) | 87/264 | 2.3 | 100% | intergenic (–/+368) | –/lnt | –/apolipoprotein N‑acyltransferase |
| ? | NODE_83 | 18 = | 0 (0.000) | coding (4/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_63 | = 6704 | 0 (0.000) | 100 (0.090) | 69/188 | 2.6 | 100% | intergenic (+323/–) | EcoliAnna_04243/– | hypothetical protein/– |
| ? | NODE_83 | = 1069 | 0 (0.000) | intergenic (+74/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_69 | 1 = | 0 (0.000) | 146 (0.860) +45 bp |
86/208 | 1.1 | 100% | noncoding (72/72 nt) | EcoliAnna_04270 | tRNA‑Val |
| ? | NODE_69 | = 77 | NA (NA) | intergenic (‑5/+40) | EcoliAnna_04270/EcoliAnna_04271 | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NODE_7 | = 176164 | 7 (0.020) | 197 (0.390) +31 bp |
117/236 | 2.7 | 98.6% | intergenic (‑4/–) | EcoliAnna_01514/– | RHS element protein/– |
| ? | NODE_93 | = 667 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_7 | = 176166 | 0 (0.000) | 679 (1.320) +29 bp |
144/240 | 1.0 | 100% | intergenic (‑6/–) | EcoliAnna_01514/– | RHS element protein/– |
| ? | NODE_93 | = 667 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_73 | = 2343 | 0 (0.000) | 157 (0.140) | 87/186 | 0.9 | 100% | intergenic (+35/–) | ltrA/– | Group II intron‑encoded protein LtrA/– |
| ? | NODE_83 | = 1068 | 0 (0.000) | intergenic (+73/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_8 | 1 = | 0 (0.000) | 140 (0.090) | 85/252 | 2.9 | 100% | intergenic (–/+54) | –/EcoliAnna_01515 | –/glycosyltransferase |
| ? | NODE_83 | 24 = | 0 (0.000) | coding (10/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_9 | = 7600 | 262 (0.900) | 69 (0.890) +109 bp |
34/80 | 1.8 | 50.5% | intergenic (+77/+123) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE |
| ? | NODE_9 | 7611 = | 242 (0.830) | intergenic (+88/+112) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE | |||||