mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 167,520 | IS2 (–) +5 bp | coding (37‑41/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,149,615 | G→T | D457E (GAC→GAA) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,721,243 | G→A | G431R (GGA→AGA) | pka → | protein lysine acetyltransferase |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,625,592 | Δ95,041 bp | IS150‑mediated | yhhJ–[mokA] | 82 genes yhhJ, rbbA, yhiI, yhiJ, yhiL, yhiL, yhiM, yhiN, pitA, uspB, uspA, dtpB, rsmJ, prlC, rlmJ, gor, dinQ, agrA, agrB, arsR, arsB, arsC, yhiS, insH1, yhiS, slp, dctR, yhiD, hdeB, hdeA, hdeD, arrS, gadE, mdtE, mdtF, gadW, gadY, gadX, gadA, yhjA, treF, yhjB, yhjC, yhjD, yhjE, yhjG, yhjH, kdgK, yhjJ, dctA, yhjK, bcsC, bcsZ, bcsB, bcsA, bcsQ, yhjR, bcsE, bcsF, bcsG, ldrD, rdlD, yhjV, dppF, dppD, dppC, dppB, dppA, proK, eptB, yhjX, yhjY, tag, yiaC, bisC, yiaD, ghrB, yiaF, yiaG, cspA, hokA, [mokA] |
| RA | 3,768,131 | A→T | pseudogene (911/945 nt) | rhsJ → | Rhs‑family protein |
| RA | 3,964,929 | C→T | E234E (GAG→GAA) | rhlB ← | ATP‑dependent RNA helicase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 123045 | 127551 | 4507 | 11 [9] | [9] 10 | [aceE]–[aceF] | [aceE],[aceF] |
| * | * | ÷ | NC_000913 | 1196253 | 1211447 | 15195 | 11 [9] | [9] 10 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423776–3424234 | 3424580–3424238 | 5–805 | 10 [8] | [9] 10 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 905931 = | 41 (1.010) | 2131 (55.280) | 268/242 | 0.0 | 98.6% | coding (823/1014 nt) | ybjS | putative NAD(P)H‑dependent oxidoreductase |
| ? | NC_000913 | = 912978 | 21 (0.540) | coding (837/1653 nt) | hcp | hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases | |||||
| * | ? | NC_000913 | 911147 = | NA (NA) | 22 (0.590) | 17/236 | 1.2 | NA | noncoding (1/26 nt) | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 911173 = | NA (NA) | intergenic (‑124/+9) | poxB/hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent | |||||
| * | ? | NC_000913 | = 911155 | NA (NA) | 22 (0.590) | 18/236 | 1.1 | NA | noncoding (9/26 nt) | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 911163 | NA (NA) | noncoding (17/26 nt) | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP84 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 32 (0.820) | 31/246 | 0.3 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||