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 |
| Marginal read alignment evidence (highest frequency 20 of 104 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 580,498 | 0 | G | A | 67.1% | 29.6 / 90.2 | 82 | V148I (GTT→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,425 | 0 | T | A | 57.5% | 86.5 / 113.2 | 81 | G123G (GGT→GGA) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,431 | 0 | T | A | 56.9% | 56.3 / 79.1 | 51 | I125I (ATT→ATA) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,437 | 0 | T | C | 56.5% | 23.4 / 27.0 | 23 | S127S (AGT→AGC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,634,017 | 0 | A | T | 55.3% | 50.5 / 64.7 | 38 | pseudogene (375/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,509 | 0 | G | C | 53.7% | 173.6 / 271.7 | 149 | L151L (CTG→CTC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,512 | 0 | A | G | 53.0% | 138.4 / 223.4 | 151 | K152K (AAA→AAG) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,518 | 0 | T | C | 52.0% | 168.6 / 275.2 | 177 | D154D (GAT→GAC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,513 | 0 | C | A | 51.0% | 189.8 / 279.6 | 157 | R153R (CGG→AGG) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,429 | 0 | A | G | 50.9% | 72.1 / 83.5 | 57 | I125V (ATT→GTT) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,524 | 0 | C | T | 50.8% | 220.0 / inf | 183 | I156I (ATC→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,514 | 0 | G | A | 50.3% | 196.1 / 285.2 | 159 | R153Q (CGG→CAG) ‡ | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,422 | 0 | A | C | 49.5% | 132.6 / 185.5 | 95 | A122A (GCA→GCC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,344 | 0 | G | A | 48.9% | 138.8 / inf | 501 | Q163Q (CAG→CAA) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,634,019 | 0 | T | C | 48.8% | 69.3 / 69.6 | 43 | pseudogene (373/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,949,356 | 0 | T | C | 48.4% | 80.6 / inf | 533 | S167S (AGT→AGC) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,359 | 0 | C | T | 47.2% | 165.1 / inf | 530 | I168I (ATC→ATT) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,419 | 0 | C | G | 46.5% | 162.7 / 188.4 | 101 | I121M (ATC→ATG) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,362 | 0 | C | T | 46.1% | 263.9 / inf | 527 | N169N (AAC→AAT) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,747 | 0 | G | A | 44.5% | 328.0 / inf | 512 | pseudogene (171/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4540713 | 232 (0.780) | 77 (0.280) | 61/182 | 12.2 | 27.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4541009 | 200 (0.740) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4540705 = | 226 (0.760) | 65 (0.240) | 53/182 | 14.8 | 24.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4541019 = | 206 (0.760) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 1041238 | NA (NA) | 4 (0.010) | 4/180 | 43.3 | 1.4% | noncoding (31/34 nt) | REP90 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP90 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 2863608 = | 288 (1.080) | coding (486/1365 nt) | ygbN | putative transporter | |||||
| * | ? | NC_000913 | = 2115728 | 300 (1.010) | 3 (0.010) | 3/172 | 43.5 | 1.2% | coding (701/1281 nt) | wcaK | colanic acid biosynthesis protein |
| ? | NC_000913 | = 2454891 | 240 (0.940) | intergenic (‑57/+146) | sixA/fadJ | phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase | |||||
| * | ? | NC_000913 | 123173 = | 334 (1.120) | 4 (0.010) | 4/184 | 43.9 | 1.4% | coding (157/2664 nt) | aceE | pyruvate dehydrogenase, decarboxylase component E1, thiamin‑binding |
| ? | NC_000913 | 266691 = | 274 (1.000) | coding (539/822 nt) | yafZ | CP4‑6 prophage; conserved protein | |||||
| * | ? | NC_000913 | = 2206843 | 260 (0.870) | 3 (0.010) | 3/176 | 44.0 | 1.2% | coding (855/1137 nt) | yehP | hypothetical protein |
| ? | NC_000913 | = 2731231 | 268 (1.030) | coding (965/2574 nt) | clpB | protein disaggregation chaperone | |||||
| * | ? | NC_000913 | 1592120 = | 239 (0.800) | 3 (0.010) | 3/176 | 44.0 | 1.2% | pseudogene (3892/5323 nt) | yneO | pseudogene, AidA homolog |
| ? | NC_000913 | = 1755979 | 288 (1.100) | coding (771/1005 nt) | ynhG | murein L,D‑transpeptidase | |||||
| * | ? | NC_000913 | 2578811 = | 292 (0.980) | 3 (0.010) | 3/178 | 44.3 | 1.0% | coding (1154/2004 nt) | tktB | transketolase 2, thiamin‑binding |
| ? | NC_000913 | 4010337 = | 308 (1.170) | coding (503/954 nt) | metR | DNA‑binding transcriptional activator, homocysteine‑binding | |||||
| * | ? | NC_000913 | 2116282 = | 292 (0.980) | 3 (0.010) | 3/178 | 44.3 | 1.1% | coding (147/1281 nt) | wcaK | colanic acid biosynthesis protein |
| ? | NC_000913 | 4192345 = | 275 (1.040) | coding (1778/1896 nt) | thiC | thiamin (pyrimidine moiety) biosynthesis protein | |||||
| * | ? | NC_000913 | = 1141454 | 343 (1.150) | 3 (0.010) | 3/178 | 44.3 | 1.1% | coding (2137/3186 nt) | rne | fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein |
| ? | NC_000913 | 2007065 = | 253 (0.960) | coding (765/1206 nt) | yedE | putative inner membrane protein | |||||