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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 4,420,589 | 0 | G | A | 41.9% | 100.3 / 212.0 | 155 | V303V (GTG→GTA) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | CP009273 | 1,198,432 | 0 | G | T | 35.2% | 111.4 / 133.9 | 128 | intergenic (‑43/‑48) | cohE/croE | e14 prophage; repressor protein phage e14/e14 prophage; putative DNA‑binding transcriptional regulator |
| * | CP009273 | 3,310,502 | 0 | A | C | 33.1% | 221.1 / 139.7 | 151 | D128E (GAT→GAG) | nusA | transcription termination/antitermination L factor |
| * | CP009273 | 2,170,734 | 0 | G | T | 31.9% | 187.6 / 74.2 | 192 | intergenic (‑51/+257) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 104,041 | 0 | G | T | 28.2% | 168.0 / 36.1 | 104 | intergenic (+80/‑151) | lpxC/secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| * | CP009273 | 2,178,908 | 0 | T | G | 26.6% | 243.0 / 28.3 | 124 | intergenic (‑128/+95) | thiM/rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
| * | CP009273 | 838,652 | 0 | T | G | 24.8% | 277.1 / 26.0 | 149 | F289V (TTT→GTT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 4,402,598 | 0 | C | G | 24.6% | 309.5 / 25.3 | 125 | S132C (TCT→TGT) | yjfM | DUF1190 family protein |
| * | CP009273 | 838,658 | 0 | G | T | 24.3% | 242.9 / 26.7 | 144 | A291S (GCC→TCC) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 2,998,314 | 0 | C | A | 23.8% | 249.9 / 13.2 | 130 | V278F (GTT→TTT) | ygeV | putative sigma‑54‑interacting transcriptional activator |
| * | CP009273 | 104,042 | 0 | A | T | 22.8% | 237.7 / 34.7 | 103 | intergenic (+81/‑150) | lpxC/secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| * | CP009273 | 2,998,305 | 0 | G | T | 22.3% | 275.4 / 20.6 | 157 | Q281K (CAA→AAA) | ygeV | putative sigma‑54‑interacting transcriptional activator |
| * | CP009273 | 3,997,395 | 0 | G | C | 21.4% | 337.2 / 20.9 | 138 | F48L (TTC→TTG) | rarD | putative chloramphenical resistance permease |
| * | CP009273 | 703,471 | 0 | T | A | 21.1% | 282.4 / 11.0 | 110 | intergenic (+258/‑319) | glnS/chiP | glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars |
| * | CP009273 | 763,412 | 0 | C | A | 21.1% | 281.3 / 11.7 | 133 | P658Q (CCA→CAA) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| * | CP009273 | 2,475,299 | 0 | C | A | 21.0% | 323.1 / 25.8 | 157 | M119I (ATG→ATT) | emrY | putative multidrug efflux system |
| * | CP009273 | 68,486 | 0 | T | G | 20.5% | 351.4 / 15.6 | 161 | L217V (TTG→GTG) | yabI | DedA family inner membrane protein |
| * | CP009273 | 4,402,608 | 0 | G | T | 20.5% | 268.6 / 11.2 | 127 | L135F (TTG→TTT) | yjfM | DUF1190 family protein |
| * | CP009273 | 838,672 | 0 | G | T | 20.3% | 276.4 / 27.4 | 149 | M295I (ATG→ATT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 776825 = | 179 (1.020) | 37 (0.210) +G |
4/266 | 10.3 | 18.9% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | CP009273 | = 2514486 | 140 (0.800) | noncoding (214/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | 4385920 = | 146 (0.830) | 4 (0.020) | 3/248 | 10.5 | 2.9% | coding (39/1338 nt) | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| ? | CP009273 | = 4385916 | 133 (0.820) | coding (35/1338 nt) | amiB | N‑acetylmuramoyl‑l‑alanine amidase II | |||||
| * | ? | CP009273 | = 4138538 | 224 (1.280) | 3 (0.020) | 3/260 | 10.8 | 1.3% | coding (1656/1734 nt) | eptC | LPS heptose I phosphoethanolamine transferase |
| ? | CP009273 | = 4239463 | 239 (1.400) | intergenic (+224/‑19) | lamB/malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein | |||||
| * | ? | CP009273 | = 3619698 | 193 (1.100) | 5 (0.030) | 3/258 | 10.8 | 2.6% | coding (466/1125 nt) | yhhJ | inner membrane putative ABC transporter permease |
| ? | CP009273 | = 3646525 | NA (NA) | noncoding (66/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 110660 | 259 (1.480) | 3 (0.020) | 3/260 | 10.8 | 1.4% | coding (730/1044 nt) | guaC | GMP reductase |
| ? | CP009273 | 3743654 = | 157 (0.920) | coding (209/696 nt) | sgbE | L‑ribulose‑5‑phosphate 4‑epimerase | |||||
| * | ? | CP009273 | 977243 = | 145 (0.830) | 4 (0.020) | 3/266 | 11.0 | 2.5% | coding (741/1848 nt) | ldtD | murein L,D‑transpeptidase |
| ? | CP009273 | = 979160 | 171 (0.980) | coding (55/648 nt) | ycbL | putative metal‑binding enzyme | |||||
| * | ? | CP009273 | = 416365 | 193 (1.100) | 3 (0.020) | 3/268 | 11.0 | 1.4% | coding (1319/1320 nt) | brnQ | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| ? | CP009273 | = 4487133 | 234 (1.330) | pseudogene (642/1266 nt) | intB | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase | |||||