mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 3,546,391 | 0 | C | T | 71.4% | 121.0 / 61.5 | 84 | intergenic (+192/‑168) | nfuA/gntT | Fe/S biogenesis protein, putative scaffold/chaperone protein/gluconate transporter, high‑affinity GNT I system |
| * | NC_000913_3_pae_pgi | 4,158,785 | 0 | C | T | 65.2% | 97.9 / 87.2 | 93 | P99L (CCC→CTC) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_pae_pgi | 1,727,768 | 0 | G | T | 36.4% | 130.2 / 120.3 | 108 | intergenic (+12/‑69) | nemA/gloA | chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme/glyoxalase I, Ni‑dependent |
| * | NC_000913_3_pae_pgi | 2,158,976 | 0 | G | . | 31.1% | 251.1 / 141.0 | 107 | coding (591/3078 nt) | mdtC | multidrug efflux system, subunit C |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 26.5% | 292.9 / 105.2 | 136 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,792 | 0 | A | C | 26.3% | 223.3 / 108.8 | 138 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 25.4% | 243.9 / 75.5 | 126 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 460,146 | 0 | T | C | 25.2% | 170.1 / 64.2 | 99 | F420S (TTC→TCC) | lon | DNA‑binding ATP‑dependent protease La |
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 25.2% | 280.5 / 91.6 | 160 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_pgi | 1,707,440 | 0 | G | T | 21.7% | 192.3 / 46.9 | 83 | E174D (GAG→GAT) | rsxC | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| Marginal new junction evidence (lowest skew 10 of 408 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 1207805 | 50 (0.470) | 40 (0.430) | 37/240 | 3.4 | 46.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | = 1209602 | 47 (0.500) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 59 (0.550) | 27 (0.290) | 24/240 | 6.3 | 34.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 49 (0.520) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 1096961 = | 106 (1.000) | 21 (0.300) +47 bp |
14/178 | 6.9 | 23.3% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_pgi | 1097243 = | NA (NA) | intergenic (+414/+322) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_pae_pgi | 1096961 = | 106 (1.000) | 18 (0.260) +47 bp |
11/178 | 8.2 | 24.0% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_pgi | 1097062 = | 69 (0.650) | intergenic (+233/+503) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_pae_pgi | = 3736321 | NA (NA) | 18 (0.190) | 15/244 | 9.6 | NA | noncoding (168/171 nt) | REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP268 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_pae_pgi | = 3736325 | NA (NA) | intergenic (+168/+28) | xylR/bax | xylose divergent operon transcriptional activator/putative glucosaminidase | |||||
| * | ? | NC_000913_3_pae_pgi | = 3944978 | NA (NA) | 25 (0.250) | 15/260 | 10.2 | 34.4% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_pae_pgi | = 4038811 | 50 (0.470) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913_3_pae_pgi | 2727891 = | NA (NA) | 27 (0.270) | 15/260 | 10.2 | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_pgi | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | = 227052 | 45 (0.420) | 25 (0.250) | 15/260 | 10.2 | 36.8% | noncoding (1294/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | 3566202 = | 96 (0.900) | 15 (0.150) | 14/256 | 10.5 | 14.1% | coding (380/2448 nt) | glgP | glycogen phosphorylase |
| ? | NC_000913_3_pae_pgi | 3566229 = | 92 (0.920) | coding (353/2448 nt) | glgP | glycogen phosphorylase | |||||
| * | ? | NC_000913_3_pae_pgi | 1097426 = | NA (NA) | 17 (0.160) | 15/268 | 10.5 | 35.0% | intergenic (+597/+139) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_pgi | 1097455 = | 32 (0.300) | intergenic (+626/+110) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||