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 209 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,745,019 | 0 | C | G | 52.9% | 24.0 / 66.1 | 51 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 1,662,198 | 0 | C | A | 51.3% | 20.8 / inf | 224 | A548E (GCA→GAA) | ynfF | S‑ and N‑oxide reductase, A subunit, periplasmic |
| * | NC_000913 | 704,173 | 0 | C | T | 50.0% | 6.3 / 63.2 | 46 | A77V (GCG→GTG) | nagE | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| * | NC_000913 | 417,533 | 0 | T | G | 48.1% | 35.0 / 22.8 | 54 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 1,554,000 | 0 | T | G | 39.7% | 104.2 / 19.5 | 68 | Y557S (TAC→TCC) | maeA | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| * | NC_000913 | 288,382 | 0 | A | C | 39.5% | 78.3 / 12.2 | 44 | T532P (ACC→CCC) | yagH | CP4‑6 prophage; putative xylosidase/arabinosidase |
| * | NC_000913 | 766,716 | 0 | G | T | 37.2% | 78.8 / 38.1 | 51 | A245S (GCG→TCG) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| * | NC_000913 | 4,101,514 | 0 | G | T | 37.2% | 154.1 / 52.5 | 78 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 3,206,446 | 0 | C | A | 36.2% | 94.4 / 17.9 | 47 | intergenic (‑190/‑17) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 4,429,984 | 0 | T | G | 35.8% | 175.5 / 25.4 | 81 | L41V (TTG→GTG) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | NC_000913 | 3,862,677 | 0 | G | A | 35.7% | 14.8 / 11.9 | 36 | pseudogene (927/1617 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 | 433,649 | 0 | T | G | 34.9% | 72.1 / 19.6 | 83 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 34.6% | 101.4 / 32.4 | 52 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| * | NC_000913 | 766,696 | 0 | G | A | 34.4% | 25.9 / 12.1 | 32 | S238N (AGT→AAT) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| * | NC_000913 | 2,326,450 | 0 | T | G | 34.4% | 215.1 / 50.6 | 96 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,782,908 | 0 | T | G | 33.9% | 78.5 / 14.0 | 67 | T252P (ACC→CCC) | gpsA | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| * | NC_000913 | 989,917 | 0 | A | G | 32.6% | 79.6 / 12.2 | 52 | L147P (CTC→CCC) | pncB | nicotinate phosphoribosyltransferase |
| * | NC_000913 | 3,745,022 | 0 | C | T | 32.6% | 34.4 / 20.1 | 55 | G73G (GGC→GGT) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 827,507 | 0 | T | G | 32.3% | 150.3 / 12.7 | 65 | D492A (GAC→GCC) | ybhF | putative ABC transporter ATPase |
| * | NC_000913 | 540,558 | 0 | T | G | 32.2% | 185.0 / 34.5 | 90 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| Marginal new junction evidence (lowest skew 10 of 79 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608007 = | NA (NA) | 8 (0.060) | 8/250 | 9.2 | 4.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 157 (1.270) | intergenic (+175/+107) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | = 3154353 | 157 (1.050) | 6 (0.040) | 6/284 | 11.2 | 3.8% | coding (866/957 nt) | yqhC | transcriptional activator of yqhD |
| ? | NC_000913 | = 3154366 | 159 (1.130) | coding (853/957 nt) | yqhC | transcriptional activator of yqhD | |||||
| * | ? | NC_000913 | 4056496 = | NA (NA) | 5 (0.040) | 5/282 | 11.7 | 3.5% | noncoding (26/85 nt) | REP295 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP295 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 4056530 = | 139 (1.000) | noncoding (60/85 nt) | REP295 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP295 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 1287084 | 102 (0.680) | 8 (0.060) | 4/262 | 11.9 | 7.9% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | NC_000913 | 1287557 = | 98 (0.760) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 3264077 | 157 (1.050) | 4 (0.030) | 4/280 | 12.3 | 2.8% | coding (941/1332 nt) | tdcC | L‑threonine/L‑serine transporter |
| ? | NC_000913 | = 3264138 | 132 (0.950) | coding (880/1332 nt) | tdcC | L‑threonine/L‑serine transporter | |||||
| * | ? | NC_000913 | = 4108906 | 160 (1.070) | 4 (0.030) | 4/286 | 12.5 | 2.6% | coding (73/990 nt) | sbp | sulfate transporter subunit |
| ? | NC_000913 | = 4109058 | 154 (1.090) | coding (225/990 nt) | sbp | sulfate transporter subunit | |||||
| * | ? | NC_000913 | 276036 = | 135 (0.900) | 4 (0.030) | 4/284 | 12.5 | 3.1% | coding (712/1404 nt) | mmuP | CP4‑6 prophage; putative S‑methylmethionine transporter |
| ? | NC_000913 | 276298 = | 124 (0.880) | coding (974/1404 nt) | mmuP | CP4‑6 prophage; putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | = 2817942 | 133 (0.890) | 5 (0.040) | 3/262 | 12.6 | 3.9% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818078 = | 130 (1.000) | noncoding (58/77 nt) | argZ | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 1608150 | 196 (1.310) | 4 (0.030) | 4/290 | 12.6 | 2.3% | coding (873/915 nt) | yneE | bestrophin family putative inner membrane protein |
| ? | NC_000913 | = 1608267 | 156 (1.090) | coding (756/915 nt) | yneE | bestrophin family putative inner membrane protein | |||||
| * | ? | NC_000913 | = 957583 | 149 (1.000) | 4 (0.030) | 4/288 | 12.6 | 2.8% | intergenic (+129/‑70) | ycaP/serC | UPF0702 family putative inner membrane protein/3‑phosphoserine/phosphohydroxythreonine aminotransferase |
| ? | NC_000913 | = 957595 | 140 (0.980) | intergenic (+141/‑58) | ycaP/serC | UPF0702 family putative inner membrane protein/3‑phosphoserine/phosphohydroxythreonine aminotransferase | |||||