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 98 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,017 | 0 | A | T | 57.5% | 68.3 / 79.6 | 47 | 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 | 1,634,019 | 0 | T | C | 57.5% | 68.6 / 66.4 | 47 | 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 | 1,949,411 | 0 | A | C | 54.3% | 380.6 / inf | 503 | N186H (AAC→CAC) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,436 | 0 | A | G | 53.6% | 170.7 / inf | 439 | L6L (CTA→CTG) | yecE | conserved protein, UPF0759 family |
| * | NC_000913 | 1,949,410 | 0 | C | T | 53.1% | 111.9 / inf | 514 | L185L (CTC→CTT) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,356 | 0 | T | C | 53.0% | 217.6 / inf | 606 | S167S (AGT→AGC) | yecD | isochorismatase family protein |
| * | NC_000913 | 1,949,344 | 0 | G | A | 52.8% | 128.1 / inf | 581 | Q163Q (CAG→CAA) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,422 | 0 | A | C | 52.0% | 139.3 / 164.7 | 98 | A122A (GCA→GCC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,359 | 0 | C | T | 52.0% | 73.8 / inf | 597 | I168I (ATC→ATT) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,431 | 0 | T | A | 51.5% | 99.6 / 131.6 | 66 | I125I (ATT→ATA) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 1,949,362 | 0 | C | T | 51.1% | ‑5.6 / inf | 577 | N169N (AAC→AAT) | yecD | isochorismatase family protein |
| * | NC_000913 | 580,425 | 0 | T | A | 51.1% | 131.7 / 172.5 | 90 | G123G (GGT→GGA) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,498 | 0 | G | A | 50.5% | 130.2 / 183.2 | 101 | V148I (GTT→ATT) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,437 | 0 | T | C | 50.0% | 60.2 / 74.8 | 42 | S127S (AGT→AGC) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,777 | 0 | C | T | 49.3% | 33.8 / inf | 584 | pseudogene (201/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,783 | 0 | C | A | 49.3% | 289.0 / inf | 574 | pseudogene (207/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,419 | 0 | C | G | 49.1% | 172.0 / 199.8 | 106 | I121M (ATC→ATG) | nohD | DLP12 prophage; DNA packaging protein |
| * | NC_000913 | 580,792 | 0 | G | C | 48.4% | 39.3 / inf | 587 | pseudogene (216/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 580,773 | 0 | G | A | 48.3% | 92.9 / inf | 566 | pseudogene (197/309 nt) | aaaD | DLP12 prophage; predicted tail fiber assembly protein (pseudogene);Phage or Prophage Related |
| * | NC_000913 | 1,634,023 | 0 | A | T | 48.2% | 99.6 / 100.9 | 56 | pseudogene (369/528 nt) | nohQ | pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin |
| 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 | = 4540713 | 427 (1.420) | 19 (0.070) | 19/180 | 16.6 | 4.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4541009 | 371 (1.360) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 4540705 = | 430 (1.430) | 21 (0.080) | 18/180 | 17.0 | 5.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4541019 = | 371 (1.360) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 291525 | 380 (1.270) | 4 (0.010) | 4/178 | 25.1 | 1.1% | intergenic (+70/+21) | yagJ/yagK | CP4‑6 prophage; putative protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| ? | NC_000913 | = 291526 | 356 (1.320) | intergenic (+71/+20) | yagJ/yagK | CP4‑6 prophage; putative protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein | |||||
| * | ? | NC_000913 | 263298 = | 268 (0.890) | 3 (0.010) | 3/180 | 26.1 | 1.2% | coding (174/222 nt) | ykfH | hypothetical protein |
| ? | NC_000913 | 2910048 = | 265 (0.970) | coding (1626/2235 nt) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase | |||||
| * | ? | NC_000913 | = 3869168 | 270 (0.900) | 3 (0.010) | 3/190 | 26.7 | 1.1% | coding (586/1293 nt) | dgoT | D‑galactonate transporter |
| ? | NC_000913 | = 3869177 | 266 (0.920) | coding (577/1293 nt) | dgoT | D‑galactonate transporter | |||||
| * | ? | NC_000913 | = 1615933 | 284 (0.950) | 5 (0.020) | 3/194 | 27.0 | 1.9% | coding (882/1191 nt) | ydeA | arabinose efflux transporter, arabinose‑inducible |
| ? | NC_000913 | = 2945543 | 241 (0.820) | noncoding (25/77 nt) | metW | tRNA‑Met | |||||