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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 31.0% | 489.4 / 291.2 | 374 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 3,156,590 | 0 | C | A | 23.9% | 464.6 / 120.5 | 209 | intergenic (+72/‑33) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| * | NC_000913 | 2,971,146 | 0 | T | C | 23.8% | 399.1 / 128.3 | 229 | intergenic (+13/‑125) | ygdQ/ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| * | NC_000913 | 710,170 | 0 | C | T | 23.6% | 471.4 / 140.5 | 249 | intergenic (+54/+30) | chiQ/fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| * | NC_000913 | 2,971,159 | 0 | G | A | 23.4% | 417.3 / 113.7 | 224 | intergenic (+26/‑112) | ygdQ/ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| * | NC_000913 | 1,985,112 | 0 | C | G | 23.1% | 341.7 / 93.9 | 156 | intergenic (‑43/+27) | araG/araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,156,591 | 0 | T | G | 22.9% | 389.8 / 136.1 | 210 | intergenic (+73/‑32) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| * | NC_000913 | 710,173 | 0 | A | G | 22.6% | 461.8 / 147.3 | 257 | intergenic (+57/+27) | chiQ/fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| * | NC_000913 | 2,971,154 | 0 | G | A | 22.6% | 464.6 / 127.6 | 236 | intergenic (+21/‑117) | ygdQ/ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| * | NC_000913 | 2,971,151 | 0 | T | C | 22.3% | 440.1 / 132.2 | 239 | intergenic (+18/‑120) | ygdQ/ygdR | UPF0053 family inner membrane protein/DUF903 family verified lipoprotein |
| * | NC_000913 | 120,158 | 1 | . | A | 21.9% | 537.8 / 219.0 | 219 | intergenic (+23/+20) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| * | NC_000913 | 2,560,321 | 0 | C | T | 21.8% | 365.5 / 100.2 | 189 | A22V (GCT→GTT) | yffL | CPZ‑55 prophage; uncharacterized protein |
| * | NC_000913 | 2,810,872 | 0 | C | T | 21.7% | 406.2 / 94.1 | 205 | H35Y (CAC→TAC) | mprA | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| * | NC_000913 | 120,154 | 0 | T | . | 21.4% | 611.9 / 172.0 | 225 | intergenic (+19/+24) | ampE/aroP | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation/aromatic amino acid transporter |
| * | NC_000913 | 4,520,500 | 0 | A | . | 21.2% | 731.7 / 204.0 | 270 | intergenic (‑176/+171) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913 | 2,810,873 | 0 | A | G | 21.2% | 385.4 / 104.6 | 205 | H35R (CAC→CGC) | mprA | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| * | NC_000913 | 4,520,504 | 1 | . | T | 21.0% | 754.4 / 260.4 | 272 | intergenic (‑180/+167) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| * | NC_000913 | 2,560,326 | 0 | A | G | 20.9% | 391.5 / 101.2 | 196 | T24A (ACA→GCA) | yffL | CPZ‑55 prophage; uncharacterized protein |
| * | NC_000913 | 4,307,290 | 0 | T | C | 20.9% | 368.8 / 95.4 | 197 | G170G (GGA→GGG) | alsK | D‑allose kinase |
| * | NC_000913 | 2,560,317 | 0 | A | C | 20.7% | 398.0 / 118.4 | 198 | N21H (AAT→CAT) | yffL | CPZ‑55 prophage; uncharacterized protein |
| Marginal new junction evidence (lowest skew 10 of 1603 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 168 (1.540) +44 bp |
14/108 | 11.4 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 618054 = | 192 (0.970) | 33 (0.190) | 20/170 | 15.4 | 16.3% | intergenic (+16/‑200) | entF/fepE | enterobactin synthase multienzyme complex component, ATP‑dependent/regulator of length of O‑antigen component of lipopolysaccharide chains |
| ? | NC_000913 | 618087 = | 173 (1.000) | intergenic (+49/‑167) | entF/fepE | enterobactin synthase multienzyme complex component, ATP‑dependent/regulator of length of O‑antigen component of lipopolysaccharide chains | |||||
| * | ? | NC_000913 | 3083831 = | 218 (1.100) | 38 (0.210) | 21/178 | 15.7 | 16.2% | intergenic (‑34/+104) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding |
| ? | NC_000913 | 3083868 = | 195 (1.080) | intergenic (‑71/+67) | speB/speA | agmatinase/biosynthetic arginine decarboxylase, PLP‑binding | |||||
| * | ? | NC_000913 | = 1287695 | 201 (1.010) | 19 (0.160) +40 bp |
9/116 | 15.8 | 13.3% | intergenic (‑73/+87) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate hydrolase |
| ? | NC_000913 | 4175472 = | 217 (1.090) | noncoding (1/85 nt) | tyrU | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 96 (0.520) | 20/182 | 16.6 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 1097101 | NA (NA) | 77 (0.420) | 19/180 | 17.0 | NA | intergenic (+272/+464) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097105 | NA (NA) | intergenic (+276/+460) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 2066558 = | NA (NA) | 60 (0.330) | 19/182 | 17.1 | 100% | noncoding (796/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2066607 = | 0 (0.000) | noncoding (747/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274347 = | NA (NA) | 60 (0.330) | 19/182 | 17.1 | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 224059 = | NA (NA) | 95 (0.520) | 19/182 | 17.1 | NA | noncoding (289/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 224082 = | NA (NA) | noncoding (312/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 226707 | NA (NA) | 90 (0.470) | 20/188 | 17.2 | NA | noncoding (949/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 226725 | NA (NA) | noncoding (967/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||