mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 233 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 417,533 | 0 | T | G | 66.7% | 3.7 / 28.5 | 51 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 3,862,664 | 0 | C | G | 56.1% | ‑3.8 / 32.9 | 42 | pseudogene (940/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 2,151,686 | 0 | G | T | 46.4% | 0.2 / 11.8 | 29 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 3,745,003 | 0 | A | G | 40.7% | 82.1 / 17.4 | 59 | E67G (GAA→GGA) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,665,702 | 0 | C | A | 38.6% | 131.7 / 38.1 | 70 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 1,554,000 | 0 | T | G | 38.5% | 146.3 / 15.3 | 97 | Y557S (TAC→TCC) | maeA | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| * | NC_000913 | 4,101,514 | 0 | G | T | 38.5% | 135.3 / 53.6 | 78 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 433,649 | 0 | T | G | 38.4% | 87.4 / 22.3 | 99 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,862,667 | 0 | G | A | 38.1% | 42.6 / 15.0 | 42 | pseudogene (937/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 354,288 | 0 | T | G | 37.5% | 93.4 / 18.5 | 48 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 2,684,779 | 0 | A | C | 36.5% | 81.0 / 18.3 | 76 | G243G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 36.3% | 222.1 / 35.6 | 103 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,745,019 | 0 | C | G | 35.7% | 55.6 / 16.5 | 56 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,206,446 | 0 | C | A | 34.7% | 144.8 / 30.0 | 76 | intergenic (‑190/‑17) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 4,101,539 | 0 | T | A | 34.1% | 190.2 / 26.1 | 86 | intergenic (+109/‑151) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 2,483,268 | 0 | T | A | 33.9% | 120.0 / 26.4 | 65 | L24F (TTA→TTT) | emrK | multidrug resistance efflux pump membrane fusion protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 33.6% | 243.3 / 66.6 | 134 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 884,184 | 0 | A | G | 33.3% | 107.3 / 10.6 | 75 | E171G (GAG→GGG) | mdfA | multidrug efflux system protein |
| * | NC_000913 | 3,760,384 | 0 | A | C | 32.8% | 110.8 / 10.1 | 65 | V289G (GTG→GGG) | selA | selenocysteine synthase |
| * | NC_000913 | 811,721 | 0 | T | G | 32.7% | 226.4 / 18.9 | 110 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 220 (1.290) | 41 (0.260) | 31/332 | 3.1 | 19.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 146 (0.940) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 214 (1.250) | 33 (0.210) | 30/332 | 3.3 | 16.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 143 (0.920) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 566774 | 257 (1.500) | 16 (0.090) | 14/360 | 6.5 | 6.3% | pseudogene (91/93 nt) | renD | pseudogene, DLP12 prophage;Phage or Prophage Related |
| ? | NC_000913 | 568036 = | 223 (1.320) | pseudogene (2/213 nt) | renD | pseudogene, DLP12 prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2595193 | 146 (0.850) | 6 (0.040) | 5/346 | 9.4 | 4.4% | coding (667/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase |
| ? | NC_000913 | = 2595247 | 123 (0.760) | coding (613/2016 nt) | tmcA | elongator methionine tRNA (ac4C34) acetyltransferase | |||||
| * | ? | NC_000913 | 141977 = | NA (NA) | 5 (0.030) | 5/346 | 9.4 | NA | intergenic (+10/+31) | hpt/can | hypoxanthine phosphoribosyltransferase/carbonic anhydrase |
| ? | NC_000913 | 142000 = | NA (NA) | intergenic (+33/+8) | hpt/can | hypoxanthine phosphoribosyltransferase/carbonic anhydrase | |||||
| * | ? | NC_000913 | 88432 = | 213 (1.250) | 6 (0.040) | 5/350 | 9.4 | 3.3% | coding (405/1005 nt) | cra | transcriptional repressor‑activator for carbon metabolism |
| ? | NC_000913 | 88504 = | 143 (0.870) | coding (477/1005 nt) | cra | transcriptional repressor‑activator for carbon metabolism | |||||
| * | ? | NC_000913 | 4519650 = | 202 (1.180) | 4 (0.020) | 4/346 | 9.9 | 2.2% | coding (675/987 nt) | yjhU | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element |
| ? | NC_000913 | 4519762 = | 166 (1.020) | coding (563/987 nt) | yjhU | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element | |||||
| * | ? | NC_000913 | = 4081273 | 153 (0.900) | 4 (0.020) | 4/346 | 9.9 | 2.6% | coding (588/636 nt) | fdoI | formate dehydrogenase‑O, cytochrome b556 subunit |
| ? | NC_000913 | = 4081294 | 160 (0.990) | coding (567/636 nt) | fdoI | formate dehydrogenase‑O, cytochrome b556 subunit | |||||
| * | ? | NC_000913 | 1323539 = | 188 (1.100) | 4 (0.020) | 4/346 | 9.9 | 2.3% | coding (320/882 nt) | yciV | PHP domain protein |
| ? | NC_000913 | 1323564 = | 163 (1.000) | coding (345/882 nt) | yciV | PHP domain protein | |||||
| * | ? | NC_000913 | 716906 = | 205 (1.200) | 5 (0.030) | 4/344 | 9.9 | 2.4% | intergenic (‑36/+40) | ybfI/potE | pseudogene/putrescine/proton symporter: putrescine/ornithine antiporter |
| ? | NC_000913 | 716932 = | 207 (1.280) | intergenic (‑62/+14) | ybfI/potE | pseudogene/putrescine/proton symporter: putrescine/ornithine antiporter | |||||