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 443 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,906,011 | 0 | T | G | 57.8% | 52.2 / 78.1 | 64 | T275P (ACC→CCC) | htpX | protease HtpX |
| * | NZ_CP009273 | 1,906,007 | 0 | T | G | 56.2% | 61.0 / 79.0 | 64 | H276P (CAC→CCC) | htpX | protease HtpX |
| * | NZ_CP009273 | 1,092,675 | 0 | A | G | 54.5% | 2.2 / 12.3 | 11 | noncoding (121/137 nt) | BW25113_RS23065 | RtT sRNA |
| * | NZ_CP009273 | 822,955 | 0 | T | G | 54.0% | 48.4 / 72.8 | 50 | T495P (ACC→CCC) | ybhF | ATP‑binding cassette domain‑containing protein |
| * | NZ_CP009273 | 1,152,727 | 0 | T | G | 54.0% | 59.9 / 80.4 | 50 | G165G (GGT→GGG) | ycfH | metal‑dependent hydrolase |
| * | NZ_CP009273 | 353,601 | 0 | C | A | 53.7% | 27.9 / 65.7 | 54 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 53.6% | 2.6 / 36.9 | 28 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 52.9% | 71.0 / 196.9 | 137 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 349,999 | 0 | T | G | 50.5% | 96.0 / 150.1 | 91 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NZ_CP009273 | 3,571,661 | 0 | A | C | 50.0% | 112.6 / 14.9 | 76 | G142G (GGT→GGG) | gntR | gluconate operon transcriptional repressor GntR |
| * | NZ_CP009273 | 4,594,167 | 0 | C | T | 49.6% | 94.4 / 101.6 | 137 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 700,996 | 0 | C | A | 49.2% | 59.3 / 38.6 | 65 | P533T (CCG→ACG) | nagE | PTS N‑acetyl glucosamine transporter subunit IIABC |
| * | NZ_CP009273 | 1,819,318 | 0 | G | A | 49.1% | 37.6 / 41.2 | 57 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy |
| * | NZ_CP009273 | 2,621,984 | 0 | A | C | 49.1% | 67.2 / 18.1 | 57 | V105G (GTC→GGC) | pdeF | cyclic‑guanylate‑specific phosphodiesterase PdeF |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 49.0% | 111.9 / 78.2 | 104 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 822,963 | 0 | T | G | 48.1% | 53.7 / 33.8 | 54 | D492A (GAC→GCC) | ybhF | ATP‑binding cassette domain‑containing protein |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 46.7% | 36.6 / 57.9 | 60 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 497,020 | 0 | A | C | 46.3% | 88.7 / 33.6 | 67 | *559E (TAA→GAA) | ybaL | Kef family K(+) transporter |
| * | NZ_CP009273 | 701,009 | 0 | T | A | 45.8% | 32.1 / 34.7 | 48 | I537N (ATC→AAC) | nagE | PTS N‑acetyl glucosamine transporter subunit IIABC |
| * | NZ_CP009273 | 1,819,313 | 0 | G | A | 45.5% | 48.4 / 33.9 | 55 | intergenic (‑119/+84) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | = 4532507 | 11 (0.110) | 10 (0.110) | 9/148 | 2.8 | 16.6% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 91 (0.980) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 11 (0.110) | 11 (0.120) | 9/148 | 2.8 | 17.9% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 91 (0.980) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4047497 | 110 (1.060) | 3 (0.030) | 3/148 | 4.5 | 3.3% | coding (1142/1410 nt) | glnG | nitrogen regulation protein NR(I) |
| ? | NZ_CP009273 | = 4047517 | 79 (0.850) | coding (1122/1410 nt) | glnG | nitrogen regulation protein NR(I) | |||||
| * | ? | NZ_CP009273 | = 3769084 | 156 (1.500) | 3 (0.030) | 3/146 | 4.5 | 2.1% | coding (153/588 nt) | mtlR | mannitol operon repressor MtlR |
| ? | NZ_CP009273 | = 3769168 | 143 (1.560) | coding (237/588 nt) | mtlR | mannitol operon repressor MtlR | |||||
| * | ? | NZ_CP009273 | 221943 = | NA (NA) | 3 (0.030) | 3/148 | 4.5 | NA | noncoding (76/77 nt) | BW25113_RS01015 | tRNA‑Ile |
| ? | NZ_CP009273 | 221964 = | NA (NA) | intergenic (+20/‑23) | BW25113_RS01015/BW25113_RS01020 | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NZ_CP009273 | = 2955064 | 99 (0.950) | 3 (0.030) | 3/160 | 4.7 | 3.0% | coding (724/3369 nt) | recC | exodeoxyribonuclease V subunit gamma |
| ? | NZ_CP009273 | = 2955068 | 97 (0.970) | coding (720/3369 nt) | recC | exodeoxyribonuclease V subunit gamma | |||||