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_34 | 1 | 46 | 46 | NA [0] | [0] 207 | –/dppA | –/dipeptide ABC transporter substrate‑binding protein DppA |
| * | * | ÷ | NODE_52 | 1 | 55 | 55 | NA [0] | [2] 236 | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR |
| * | * | ÷ | NODE_57 | 12827 | 12883 | 57 | 179 [0] | [0] NA | argE/– | acetylornithine deacetylase/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NODE_13 | = 114251 | 0 (0.000) | 114 (0.130) | 74/184 | 1.0 | 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) | 179 (1.070) +46 bp |
96/206 | 0.7 | 100% | intergenic (–/‑68) | –/EcoliAnna_02239 | –/hypothetical protein |
| ? | NODE_35 | 1 = | 0 (0.000) | noncoding (1/76 nt) | EcoliAnna_03558 | tRNA‑Asp | |||||
| * | ? | NODE_17 | = 67973 | 278 (1.150) | 46 (0.770) +112 bp |
28/74 | 1.5 | 39.3% | intergenic (‑80/+78) | nrdG/nrdD | anaerobic ribonucleoside‑triphosphate reductase‑activating protein/anaerobic ribonucleoside‑triphosphate reductase |
| ? | NODE_17 | 67993 = | 294 (1.220) | intergenic (‑100/+58) | nrdG/nrdD | anaerobic ribonucleoside‑triphosphate reductase‑activating protein/anaerobic ribonucleoside‑triphosphate reductase | |||||
| * | ? | NODE_17 | = 104175 | 0 (0.000) | 141 (0.160) | 93/178 | 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 | 262 (1.140) | 208 (0.910) | 140/298 | 0.6 | 44.3% | 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) | 151 (1.090) +60 bp |
69/178 | 1.6 | 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) | 130 (0.100) | 86/262 | 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) | 567 (0.630) | 192/298 | 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) | 560 (0.620) +C |
130/296 | 0.7 | 99.7% | intergenic (–/‑159) | –/EcoliAnna_00414 | –/threonine‑rich inner membrane protein GfcA |
| ? | NODE_94 | = 576 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_21 | = 66680 | 0 (0.000) | 106 (0.120) | 69/178 | 1.4 | 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) | 94 (0.620) | 68/184 | 2.4 | 100% | intergenic (–/‑451) | –/EcoliAnna_03042 | –/phosphoenolpyruvate carboxylase |
| ? | NODE_57 | = 12826 | 0 (0.000) | intergenic (+146/–) | argE/– | acetylornithine deacetylase/– | |||||
| * | ? | NODE_24 | = 58866 | 115 (0.460) | 60 (0.780) +103 bp |
33/92 | 2.5 | 64.1% | intergenic (+39/–) | rhaA/– | L‑rhamnose isomerase/– |
| ? | NODE_24 | 58878 = | 103 (0.410) | intergenic (+51/–) | rhaA/– | L‑rhamnose isomerase/– | |||||
| * | ? | NODE_25 | = 58798 | 0 (0.000) | 133 (0.150) | 80/186 | 2.0 | 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) | 129 (0.140) | 83/186 | 1.0 | 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) | 122 (0.670) | 88/206 | 1.7 | 100% | intergenic (+226/–) | EcoliAnna_03267/– | tRNA‑Pro/– |
| ? | NODE_34 | 47 = | 0 (0.000) | intergenic (–/‑684) | –/dppA | –/dipeptide ABC transporter substrate‑binding protein DppA | |||||
| * | ? | NODE_28 | 84 = | 152 (0.590) | 66 (1.110) +115 bp |
24/68 | 2.1 | 63.7% | intergenic (–/‑59) | –/rhaD | –/rhamnulose‑1‑phosphate aldolase |
| ? | NODE_53 | = 83 | 177 (0.670) | intergenic (–/+190) | –/EcoliAnna_04105 | –/NAD(P)H‑flavin reductase | |||||
| * | ? | NODE_30 | 1 = | 0 (0.000) | 138 (0.150) | 84/184 | 0.6 | 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) | 153 (1.060) | 103/188 | 0.1 | 100% | intergenic (+298/–) | codA/– | Cytosine deaminase/– |
| ? | NODE_52 | 56 = | 0 (0.000) | intergenic (–/+38) | –/oxyR_1 | –/DNA‑binding transcriptional regulator OxyR | |||||
| * | ? | NODE_38 | 1 = | 0 (0.000) | 974 (1.120) | 219/282 | 0.0 | 100% | intergenic (–/‑281) | –/EcoliAnna_03684 | –/hypothetical protein |
| ? | NODE_94 | 9 = | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_39 | = 35183 | 0 (0.000) | 108 (0.120) | 71/190 | 1.6 | 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) | 196 (0.880) +AT |
126/294 | 0.7 | 100% | intergenic (‑303/–) | ghrA/– | glyoxylate/hydroxypyruvate reductase GhrA/– |
| ? | NODE_76 | = 1792 | 0 (0.000) | intergenic (+389/–) | EcoliAnna_04287/– | hypothetical protein/– | |||||
| * | ? | NODE_44 | 1 = | 0 (0.000) | 121 (0.130) | 79/190 | 0.8 | 100% | intergenic (–/‑142) | –/wbbL_2 | –/Rhamnosyltransferase WbbL |
| ? | NODE_83 | = 1070 | 0 (0.000) | intergenic (+75/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_48 | 1 = | 0 (0.000) | 619 (0.660) | 132/190 | 0.0 | 100% | intergenic (–/+33) | –/EcoliAnna_03993 | –/hypothetical protein |
| ? | NODE_83 | = 1070 | 0 (0.000) | intergenic (+75/–) | EcoliAnna_04298/– | IS5‑like element IS5 family transposase/– | |||||
| * | ? | NODE_49 | = 25569 | 0 (0.000) | 1345 (1.060) | 205/260 | 0.0 | 100% | intergenic (‑3/–) | EcoliAnna_04040/– | hypothetical protein/– |
| ? | NODE_83 | 20 = | 0 (0.000) | coding (6/981 nt) | EcoliAnna_04298 | IS5‑like element IS5 family transposase | |||||
| * | ? | NODE_53 | = 108 | 221 (0.830) | 20 (0.860) +136 bp |
13/26 | 0.4 | 49.1% | intergenic (–/+165) | –/EcoliAnna_04105 | –/NAD(P)H‑flavin reductase |
| ? | NODE_53 | 152 = | 255 (0.960) | intergenic (–/+121) | –/EcoliAnna_04105 | –/NAD(P)H‑flavin reductase | |||||
| * | ? | NODE_55 | = 14553 | 0 (0.000) | 118 (0.100) | 78/252 | 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) | 139 (0.110) | 89/264 | 1.6 | 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) | 96 (0.100) | 64/188 | 2.9 | 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) | 151 (0.960) +45 bp |
92/208 | 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 | 11 (0.040) | 377 (0.980) +31 bp |
151/236 | 0.0 | 98.9% | intergenic (‑4/–) | EcoliAnna_01514/– | RHS element protein/– |
| ? | NODE_93 | = 667 | 0 (0.000) | intergenic (–/–) | –/– | –/– | |||||
| * | ? | NODE_73 | = 2343 | 0 (0.000) | 127 (0.140) | 76/186 | 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 | 265 (1.120) | 53 (0.840) +109 bp |
32/80 | 1.2 | 43.1% | intergenic (+77/+123) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE |
| ? | NODE_9 | 7611 = | 256 (1.080) | intergenic (+88/+112) | EcoliAnna_01666/nlpE | YaeF family permuted papain‑like enzyme/envelope stress response activation lipoprotein NlpE | |||||