mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 547,694 | A→G | pseudogene (114/1259 nt) | ylbE → | DUF1116 domain‑containing protein |
| RA | 547,835 | +G | pseudogene (255/1259 nt) | ylbE → | DUF1116 domain‑containing protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| MC JC | 654,214 | Δ1,199 bp | Y75_RS03225–[dcuC] | Y75_RS03225, [dcuC] | |
| RA | 987,574 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | porin OmpF/asparagine‑‑tRNA ligase |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | dgcT → | GGDEF domain‑containing protein |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,809 | C→T | T370T (ACC→ACT) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,822 | T→C | L375M (TTA→CTG) | icd → | NADP‑dependent isocitrate dehydrogenase |
| RA | 1,197,824 | A→G | L375M (TTA→CTG) | icd → | NADP‑dependent isocitrate dehydrogenase |
| MC JC | 1,301,041 | Δ1,336 bp | Y75_RS06530–Y75_RS06530 | Y75_RS06530, Y75_RS06530 | |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,979,957 | G→T | intergenic (‑46/+398) | flhD ← / ← Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase |
| RA | 2,005,401 | C→T | E115K (GAA→AAA) | fliC ← | H48 family flagellin FliC |
| MC JC | 2,176,983 | Δ1,199 bp | Y75_RS10980–[gatA] | Y75_RS10980, [gatA] | |
| RA | 2,245,455 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| MC JC | 2,320,795 | Δ1,336 bp | Y75_RS11650–[rcsC] | Y75_RS11650, Y75_RS11650, [rcsC] | |
| RA | 2,866,111 | A→G | pseudogene (97/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | yhaC → | YhaC family protein |
| MC JC | 3,742,936 | Δ1,336 bp | Y75_RS18560–Y75_RS18560 | Y75_RS18560, Y75_RS18560 | |
| MC JC | 3,746,911 | Δ1,199 bp | Y75_RS18585–[tnaB] | Y75_RS18585, [tnaB] | |
| MC JC | 3,750,591 | Δ1,199 bp | Y75_RS18600 | Y75_RS18600 | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | dctA → | C4‑dicarboxylate transporter DctC |
| RA | 4,005,879 | T→C | intergenic (‑305/‑78) | yhiM ← / → Y75_RS19820 | DUF2776 domain‑containing protein/YhiJ/YhiL family protein |
| MC JC | 4,310,363 | Δ1,199 bp | Y75_RS21310–[alsK] | Y75_RS21310, [alsK] | |
| RA | 4,371,274 | (A)5→3 | pseudogene (179‑180/1304 nt) | dcuA ← | anaerobic C4‑dicarboxylate transporter DcuA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 1197850 | 1213051 | 15202 | 64 [61] | [55] 66 | [icd]–[Y75_RS23470] | [icd],ymfD,Y75_RS05950,lit,intE,xisE,Y75_RS24820,Y75_RS23460,Y75_RS05970,ymfK,ymfT,ymfL,Y75_RS23465,Y75_RS25370,Y75_RS05995,Y75_RS06000,Y75_RS06005,Y75_RS06010,ymfQ,Y75_RS06020,tfaP,tfaE,Y75_RS06035,pinE,mcrA,[Y75_RS23470] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 380484 = | NA (NA) | 150 (0.920) | 80/466 | 0.3 | NA | coding (28/444 nt) | Y75_RS01845 | transferase |
| ? | NC_007779 | = 381407 | NA (NA) | coding (518/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | 381401 = | NA (NA) | 195 (1.210) | 96/462 | 0.1 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (264/264 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | 2519723 = | NA (NA) | 117 (0.730) | 62/460 | 0.8 | 93.7% | intergenic (+33/‑54) | nupC/Y75_RS12570 | nucleoside permease NupC/IS4‑like element IS421 family transposase |
| ? | NC_007779 | = 2600448 | 8 (0.050) | coding (592/618 nt) | hyfA | hydrogenase 4 subunit HyfA | |||||
| * | ? | NC_007779 | = 2521059 | NA (NA) | 132 (0.830) | 70/458 | 0.5 | 95.7% | intergenic (+170/+30) | Y75_RS12570/pdeA | IS4‑like element IS421 family transposase/sensor domain‑containing phosphodiesterase |
| ? | NC_007779 | 2600437 = | 6 (0.040) | coding (581/618 nt) | hyfA | hydrogenase 4 subunit HyfA | |||||
| * | ? | NC_007779 | = 3186081 | NA (NA) | 180 (1.110) | 90/464 | 0.1 | 98.9% | coding (26/2466 nt) | Y75_RS15850 | fimbrial biogenesis outer membrane usher protein |
| ? | NC_007779 | 3512753 = | 2 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR | |||||
| * | ? | NC_007779 | = 3261133 | 0 (0.000) | 228 (1.430) | 74/458 | 0.4 | 100% | intergenic (‑59/‑69) | tdcE/Y75_RS16205 | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 3262333 = | 0 (0.000) | pseudogene (1183/1185 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_007779 | = 3512759 | 1 (0.010) | 169 (1.040) | 84/464 | 0.2 | 99.4% | coding (535/1026 nt) | cytR | DNA‑binding transcriptional regulator CytR |
| ? | NC_007779 | = 3744262 | NA (NA) | intergenic (‑90/+31) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ | |||||
| * | ? | NC_007779 | = 3744263 | NA (NA) | 129 (0.790) | 69/466 | 0.5 | 100% | intergenic (‑91/+30) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ |
| ? | NC_007779 | 3903274 = | 0 (0.000) | coding (37/825 nt) | bax | protein bax | |||||
| * | ? | NC_007779 | = 3903279 | 2 (0.010) | 174 (1.070) | 81/464 | 0.2 | 98.9% | coding (42/825 nt) | bax | protein bax |
| ? | NC_007779 | = 4504190 | NA (NA) | intergenic (+10/+83) | Y75_RS22280/Y75_RS22285 | IS3‑like element IS2 family transposase/phosphoethanolamine transferase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 95 (0.580) | 46/466 | 1.8 | 100% | intergenic (‑287/‑68) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 0 (0.000) | intergenic (+208/+60) | yjhR/Y75_RS25450 | helicase YjhR/HNH endonuclease | |||||
| * | ? | NC_007779 | = 4311556 | NA (NA) | 229 (1.410) | 80/464 | 0.3 | 98.7% | intergenic (+145/+1) | Y75_RS21310/alsK | IS5‑like element IS5 family transposase/allose kinase |
| ? | NC_007779 | 4540915 = | 3 (0.020) | intergenic (+204/+64) | yjhR/Y75_RS25450 | helicase YjhR/HNH endonuclease | |||||