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 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,663,765 | 0 | T | A | 64.3% | 0.3 / 12.0 | 14 | I29F (ATT→TTT) | ynfL | LysR family transcriptional regulator |
| * | NZ_CP009273 | 1,906,007 | 0 | T | G | 63.6% | 15.6 / 23.0 | 22 | H276P (CAC→CCC) | htpX | protease HtpX |
| * | NZ_CP009273 | 2,738,448 | 0 | A | C | 59.3% | 18.9 / 30.3 | 27 | V84G (GTG→GGG) | trmD | tRNA (guanosine(37)‑N1)‑methyltransferase TrmD |
| * | NZ_CP009273 | 1,906,011 | 0 | T | G | 59.1% | 10.4 / 24.3 | 22 | T275P (ACC→CCC) | htpX | protease HtpX |
| * | NZ_CP009273 | 3,578,446 | 0 | A | C | 59.1% | 3.4 / 24.0 | 22 | Y580D (TAC→GAC) | ggt | gamma‑glutamyltransferase |
| * | NZ_CP009273 | 3,703,332 | 0 | A | C | 55.6% | 12.5 / 22.2 | 18 | G168G (GGT→GGG) | eptB | kdo(2)‑lipid A phosphoethanolamine 7''‑transferase |
| * | NZ_CP009273 | 353,586 | 0 | A | T | 54.5% | ‑4.4 / 11.4 | 11 | N272K (AAT→AAA) | cynR | transcriptional regulator CynR |
| * | NZ_CP009273 | 510,080 | 0 | A | C | 54.5% | 8.1 / 11.4 | 11 | V79G (GTG→GGG) | ybbJ | NfeD family protein |
| * | NZ_CP009273 | 69,900 | 0 | A | C | 54.2% | 12.1 / 22.4 | 24 | V370G (GTG→GGG) | thiP | thiamine/thiamine pyrophosphate ABC transporter permease ThiP |
| * | NZ_CP009273 | 489,981 | 0 | A | G | 53.8% | 7.8 / 13.8 | 13 | M41V (ATG→GTG) | recR | recombination mediator RecR |
| * | NZ_CP009273 | 2,388,923 | 0 | A | C | 53.3% | 30.5 / 36.5 | 30 | G151G (GGT→GGG) | nuoJ | NADH‑quinone oxidoreductase subunit J |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 53.1% | 22.8 / 68.7 | 49 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 1,429,975 | 0 | G | A | 52.9% | 7.7 / 22.3 | 17 | intergenic (‑99/+42) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NZ_CP009273 | 822,955 | 0 | T | G | 52.6% | 17.8 / 25.3 | 19 | T495P (ACC→CCC) | ybhF | ATP‑binding cassette domain‑containing protein |
| * | NZ_CP009273 | 1,598,494 | 0 | C | T | 52.6% | 9.4 / 26.6 | 19 | S64L (TCG→TTG) | lsrD | autoinducer 2 ABC transporter permease LsrD |
| * | NZ_CP009273 | 4,123,160 | 0 | A | G | 52.4% | 22.8 / 27.2 | 21 | E206G (GAA→GGA) | metF | methylenetetrahydrofolate reductase |
| * | NZ_CP009273 | 3,357,755 | 0 | A | T | 52.2% | 8.7 / 27.3 | 23 | P530P (CCA→CCT) | yhcD | fimbrial biogenesis outer membrane usher protein |
| * | NZ_CP009273 | 3,175,957 | 0 | A | T | 51.8% | 13.9 / 32.3 | 27 | I17F (ATT→TTT) | zupT | zinc transporter ZupT |
| * | NZ_CP009273 | 2,134,407 | 0 | A | C | 51.7% | 30.6 / 44.9 | 29 | G229G (GGT→GGG) | asmA | outer membrane assembly protein AsmA |
| * | NZ_CP009273 | 1,429,984 | 0 | G | A | 50.0% | 7.5 / 12.2 | 18 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| 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 | 2772304 = | 29 (0.910) | 6 (0.190) | 6/166 | 1.8 | 17.1% | coding (3782/4581 nt) | ypjA | adhesin‑like autotransporter YpjA/EhaD |
| ? | NZ_CP009273 | = 2991050 | NA (NA) | intergenic (‑91/+1) | BW25113_RS14875/BW25113_RS14890 | IS3‑like element IS2 family transposase/glycoside hydrolase family 15 protein | |||||
| * | ? | NZ_CP009273 | = 2283591 | NA (NA) | 8 (0.250) | 5/164 | 2.0 | 18.4% | intergenic (‑67/‑388) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP |
| ? | NZ_CP009273 | = 3512441 | 36 (1.130) | intergenic (‑18/+383) | aroK/hofQ | shikimate kinase AroK/DNA uptake porin HofQ | |||||
| * | ? | NZ_CP009273 | 1203246 = | 23 (0.720) | 3 (0.120) | 3/134 | 2.3 | 13.2% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | 1205075 = | 21 (0.820) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||