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 83 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,019 | 0 | T | C | 74.2% | 14.9 / 22.2 | 31 | 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 | 1,634,023 | 0 | A | T | 65.7% | 25.3 / 37.2 | 35 | pseudogene (369/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 1,634,026 | 0 | T | G | 62.2% | 31.6 / 39.6 | 37 | pseudogene (366/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,498 | 0 | G | A | 56.2% | 6.2 / 21.9 | 16 | V148I (GTT→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,634,029 | 0 | G | C | 56.1% | 43.4 / 68.8 | 41 | pseudogene (363/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| * | NC_000913 | 580,425 | 0 | T | A | 50.0% | 20.2 / 34.1 | 20 | G123G (GGT→GGA) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,344 | 0 | G | A | 49.7% | 48.4 / inf | 467 | Q163Q (CAG→CAA) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,356 | 0 | T | C | 48.0% | 19.5 / inf | 519 | S167S (AGT→AGC) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,436 | 0 | A | G | 47.6% | 38.5 / inf | 468 | L6L (CTA→CTG) | yecE | conserved protein, UPF0759 family |
| * | NC_000913 | 1,949,362 | 0 | C | T | 47.3% | 164.1 / inf | 507 | N169N (AAC→AAT) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,359 | 0 | C | T | 47.3% | 127.6 / inf | 523 | I168I (ATC→ATT) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,410 | 0 | C | T | 45.7% | 216.0 / inf | 541 | L185L (CTC→CTT) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,411 | 0 | A | C | 45.6% | 17.6 / inf | 542 | N186H (AAC→CAC) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,422 | 0 | A | C | 40.7% | 35.9 / 38.1 | 27 | A122A (GCA→GCC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,472 | 0 | G | T | 40.2% | 400.4 / inf | 291 | G18G (GGG→GGT) | yecE | conserved protein, UPF0759 family |
| * | NC_000913 | 580,509 | 0 | G | C | 40.0% | 79.8 / 67.3 | 45 | L151L (CTG→CTC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,783 | 0 | C | A | 39.3% | 743.1 / inf | 494 | pseudogene (207/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,773 | 0 | G | A | 38.9% | 533.3 / inf | 507 | pseudogene (197/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,777 | 0 | C | T | 38.8% | 507.3 / inf | 503 | pseudogene (201/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,741 | 0 | C | G | 38.6% | 515.4 / inf | 466 | pseudogene (165/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1432788 | 292 (1.070) | 6 (0.030) +CAGGCTGGCGTTCG |
3/146 | 37.1 | 2.6% | intergenic (‑540/+194) | ynaE/ttcC | cold shock protein, function unknown, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| ? | NC_000913 | = 1630540 | 240 (0.880) | intergenic (‑231/‑556) | ydfJ/ydfK | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage | |||||
| * | ? | NC_000913 | 1720640 = | 194 (0.710) | 3 (0.010) | 3/152 | 38.1 | 1.7% | coding (496/2013 nt) | ydhK | putative efflux protein (PET) component of YdhJK efflux pump |
| ? | NC_000913 | = 1720636 | 173 (0.730) | coding (492/2013 nt) | ydhK | putative efflux protein (PET) component of YdhJK efflux pump | |||||
| * | ? | NC_000913 | = 1810415 | 230 (0.840) | 3 (0.010) | 3/162 | 39.7 | 1.4% | coding (742/804 nt) | ydjO | hypothetical protein |
| ? | NC_000913 | = 1810416 | 207 (0.820) | coding (741/804 nt) | ydjO | hypothetical protein | |||||
| * | ? | NC_000913 | = 4063314 | 230 (0.840) | 3 (0.010) | 3/170 | 40.9 | 1.4% | coding (476/1404 nt) | yihO | putative transporter |
| ? | NC_000913 | = 4063328 | 213 (0.800) | coding (462/1404 nt) | yihO | putative transporter | |||||
| * | ? | NC_000913 | = 189424 | 274 (1.010) | 4 (0.010) | 3/172 | 41.2 | 1.5% | coding (83/795 nt) | map | methionine aminopeptidase |
| ? | NC_000913 | 4243642 = | 264 (0.980) | coding (801/1191 nt) | malE | maltose transporter subunit | |||||