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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| JC JC | 1,293,032 | IS1 (–) +8 bp | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 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 | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| JC JC | 4,620,780 | IS1 (–) +9 bp | coding (1178‑1186/1224 nt) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1299499 | 1300693–1299512 | 14–1195 | 39 [0] | [0] 44 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 2066285–2066464 | 2066587–2066466 | 3–303 | 4 [2] | [3] 13 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423798–3424233 | 3424520–3424240 | 8–723 | 5 [3] | [2] 4 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3514389 | 3515073 | 685 | 4 [2] | [3] 4 | [gph]–[rpe] | [gph],[rpe] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274620 = | NA (NA) | 6 (0.220) | 5/242 | 2.5 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 381663 = | NA (NA) | 4 (0.140) | 4/246 | 2.9 | NA | noncoding (404/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381703 = | NA (NA) | noncoding (444/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381669 | NA (NA) | 7 (0.250) | 7/246 | 2.0 | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382242 | NA (NA) | 4 (0.140) | 4/248 | 2.9 | NA | noncoding (983/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382260 | NA (NA) | noncoding (1001/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 800912 | 11 (0.370) | 4 (0.140) | 4/250 | 2.9 | 25.3% | coding (154/1053 nt) | ybhH | putative PrpF family isomerase |
| ? | NC_000913 | = 800937 | 13 (0.460) | coding (179/1053 nt) | ybhH | putative PrpF family isomerase | |||||
| * | ? | NC_000913 | 1207790 = | 14 (0.470) | 7 (0.270) | 6/228 | 2.1 | 34.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.540) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.470) | 9 (0.350) | 9/228 | 1.5 | 40.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.540) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 36 (1.350) | 29/236 | 0.1 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 37 (1.380) | 31/236 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+1449/‑488) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2066588 = | 3 (0.100) | 5 (0.170) | 5/254 | 2.6 | 63.0% | noncoding (766/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2102216 = | NA (NA) | noncoding (728/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 11 (0.370) | 11/260 | 1.4 | 33.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3934362 = | 22 (0.750) | coding (585/1506 nt) | rbsA | D‑ribose ABC transporter ATPase | |||||
| * | ? | NC_000913 | = 3299608 | 27 (0.920) | 8 (0.290) | 4/240 | 2.8 | 23.6% | coding (308/444 nt) | yhbP | UPF0306 family protein |
| ? | NC_000913 | = 3299630 | 27 (0.990) | coding (286/444 nt) | yhbP | UPF0306 family protein | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 9 (0.310) | 7/260 | 2.2 | 33.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3934365 | 18 (0.610) | coding (588/1506 nt) | rbsA | D‑ribose ABC transporter ATPase | |||||
| * | ? | NC_000913 | 3910443 = | NA (NA) | 4 (0.140) | 4/250 | 2.9 | NA | noncoding (1/35 nt) | REP284 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP284 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 3910474 = | NA (NA) | noncoding (32/35 nt) | REP284 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP284 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||