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_10 | 108,811 | Δ1 bp | coding (87/1257 nt) | EcoliAnna_01894 → | MFS transporter |
| 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 |
| MC JC | NODE_26 | 7,555 | Δ2,934 bp | EcoliAnna_03163–[tolC_2] | EcoliAnna_03163, tetR(A), tet(A), tetC, [tolC_2] | |
| 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 | 46297 | 46324 | 28 | 192 [179] | [0] NA | rpsT/– | 30S ribosomal protein S20/– |
| * | * | ÷ | NODE_34 | 1 | 46 | 46 | NA [0] | [0] 235 | –/dppA | –/dipeptide ABC transporter substrate‑binding protein DppA |
| * | * | ÷ | NODE_52 | 1 | 55 | 55 | NA [0] | [1] 231 | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR |
| * | * | ÷ | NODE_57 | 12827 | 12883 | 57 | 229 [2] | [0] NA | argE/– | acetylornithine deacetylase/– |
| * | * | ÷ | NODE_94 | 1 | 8 | 8 | NA [0] | [0] 1155 | –/– | –/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NODE_11 | = 115859 | 220 (0.900) | 20 (0.530) +126 bp |
13/46 | 2.5 | 37.0% | intergenic (+186/+130) | EcoliAnna_02020/copA | HigA family addiction module antidote protein/copper‑exporting P‑type ATPase CopA |
| ? | NODE_11 | 115896 = | 221 (0.900) | intergenic (+223/+93) | EcoliAnna_02020/copA | HigA family addiction module antidote protein/copper‑exporting P‑type ATPase CopA | |||||
| * | ? | NODE_13 | = 114251 | 0 (0.000) | 125 (0.110) | 79/184 | 0.8 | 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) | 360 (1.110) +46 bp |
128/206 | 0.2 | 100% | intergenic (–/‑68) | –/EcoliAnna_02239 | –/hypothetical protein |
| ? | NODE_25 | 1 = | 0 (0.000) | noncoding (1/76 nt) | EcoliAnna_03094 | tRNA‑Asp | |||||
| * | ? | NODE_17 | = 104175 | 0 (0.000) | 175 (0.160) | 91/178 | 1.0 | 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 | 308 (1.160) | 258 (1.000) | 158/298 | 0.2 | 45.6% | coding (1102/1410 nt) | EcoliAnna_02682 | hypothetical protein |
| ? | NODE_66 | 4091 = | NA (NA) | coding (14/363 nt) | EcoliAnna_04262 | hypothetical protein | |||||
| * | ? | NODE_19 | 1 = | 0 (0.000) | 152 (0.090) | 90/262 | 2.4 | 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_2 | 1 = | 0 (0.000) | 633 (0.630) | 200/298 | 0.0 | 100% | intergenic (–/‑160) | –/EcoliAnna_00414 | –/threonine‑rich inner membrane protein GfcA |
| ? | NODE_94 | = 576 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_2 | 2 = | 3 (0.010) | 606 (0.610) +C |
137/296 | 0.4 | 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) | 111 (0.100) | 59/178 | 2.9 | 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) | 143 (0.730) | 86/184 | 2.2 | 100% | intergenic (–/‑451) | –/EcoliAnna_03042 | –/phosphoenolpyruvate carboxylase |
| ? | NODE_57 | = 12826 | 0 (0.000) | intergenic (+146/–) | argE/– | acetylornithine deacetylase/– | |||||
| * | ? | NODE_24 | = 58866 | 149 (0.460) | 89 (0.890) +103 bp |
38/92 | 2.9 | 67.2% | intergenic (+39/–) | rhaA/– | L‑rhamnose isomerase/– |
| ? | NODE_24 | 58878 = | 133 (0.410) | intergenic (+51/–) | rhaA/– | L‑rhamnose isomerase/– | |||||
| * | ? | NODE_25 | = 58798 | 0 (0.000) | 873 (0.680) | 159/186 | 0.1 | 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) | 151 (0.130) | 74/186 | 2.4 | 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) | 143 (0.610) | 96/206 | 2.5 | 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) | 122 (0.110) | 80/184 | 1.2 | 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) | 144 (0.880) | 94/188 | 0.5 | 100% | intergenic (+298/–) | codA/– | Cytosine deaminase/– |
| ? | NODE_52 | 56 = | 0 (0.000) | intergenic (–/+38) | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR | |||||
| * | ? | NODE_36 | = 15379 | 236 (0.950) | 29 (0.920) +130 bp |
11/38 | 2.1 | 48.5% | intergenic (+58/+137) | purK/EcoliAnna_03628 | 5‑(carboxyamino)imidazole ribonucleotide synthase/carbamate kinase |
| ? | NODE_36 | 15414 = | 246 (0.990) | intergenic (+93/+102) | purK/EcoliAnna_03628 | 5‑(carboxyamino)imidazole ribonucleotide synthase/carbamate kinase | |||||
| * | ? | NODE_38 | 1 = | 0 (0.000) | 1062 (1.070) | 220/282 | 0.0 | 100% | intergenic (–/‑281) | –/EcoliAnna_03684 | –/hypothetical protein |
| ? | NODE_94 | 9 = | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_39 | = 35183 | 0 (0.000) | 100 (0.090) | 70/190 | 1.5 | 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) | 189 (0.860) +AT |
125/294 | 0.7 | 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) | 115 (0.700) +55 bp |
60/188 | 2.6 | 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) | 134 (0.110) | 79/190 | 0.9 | 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) | 122 (0.610) | 83/196 | 2.9 | 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) | 187 (0.150) | 106/190 | 0.9 | 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 | 289 (0.980) | 22 (0.660) +132 bp |
11/34 | 2.3 | 40.2% | intergenic (+97/+84) | EcoliAnna_01167/cca | undecaprenyl‑diphosphate phosphatase/fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase Cca |
| ? | NODE_5 | 162477 = | 285 (0.970) | intergenic (+137/+44) | EcoliAnna_01167/cca | undecaprenyl‑diphosphate phosphatase/fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase Cca | |||||
| * | ? | NODE_53 | = 21980 | 0 (0.000) | 1731 (0.970) | 237/260 | 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_62 | 1 = | 0 (0.000) | 152 (0.090) | 85/264 | 2.8 | 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) | 113 (0.100) | 79/188 | 1.8 | 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) | 169 (1.000) +45 bp |
98/208 | 0.6 | 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 | 17 (0.050) | 437 (0.910) +31 bp |
158/236 | 0.2 | 98.5% | intergenic (‑4/–) | EcoliAnna_01514/– | RHS element protein/– |
| ? | NODE_93 | = 667 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_73 | = 2343 | 0 (0.000) | 147 (0.130) | 86/186 | 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_9 | = 7600 | 266 (0.980) | 85 (1.170) +109 bp |
38/80 | 0.8 | 54.6% | intergenic (+77/+123) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE |
| ? | NODE_9 | 7611 = | 260 (0.960) | intergenic (+88/+112) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE | |||||