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 |
| JC JC | 167,520 | IS2 (–) +5 bp | coding (37‑41/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| RA | 216,852 | G→A | S51F (TCT→TTT) | yaeF ← | putative lipoprotein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,023,628 | +G | coding (256/2154 nt) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| 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 | 2,173,363 | 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 | 123049 | 127550 | 4502 | 21 [19] | [18] 21 | [aceE]–[aceF] | [aceE],[aceF] |
| * | * | ÷ | NC_000913 | 3423767–3424234 | 3424544–3424238 | 5–778 | 21 [20] | [20] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 905931 = | 58 (0.620) | 3340 (37.060) | 278/272 | -0.0 | 98.4% | coding (823/1014 nt) | ybjS | putative NAD(P)H‑dependent oxidoreductase |
| ? | NC_000913 | = 912978 | 54 (0.600) | coding (837/1653 nt) | hcp | hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases | |||||
| * | ? | NC_000913 | 911147 = | NA (NA) | 54 (0.610) | 28/266 | 2.1 | 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 | 1207790 = | 11 (0.120) | 36 (0.430) | 34/252 | 1.4 | 83.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 5 (0.060) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.130) | 50 (0.600) | 46/252 | 0.7 | 86.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 5 (0.060) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 73 (0.800) | 63/276 | 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 | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 82 (0.870) | 70/284 | 0.2 | 39.8% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4337579 | 124 (1.320) | coding (351/762 nt) | adiY | adi system transcriptional activator | |||||