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 35 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,354,607 | 0 | C | A | 74.6% | 185.5 / 85.4 | 126 | V288V (GTG→GTT) | sapB | antimicrobial peptide transport ABC transporter permease |
| * | NC_000913 | 4,332,986 | 0 | G | A | 66.1% | 124.7 / 114.4 | 125 | A96V (GCG→GTG) | basS | sensory histidine kinase in two‑component regulatory system with BasR |
| * | NC_000913 | 4,277,391 | 0 | C | A | 56.4% | ‑6.4 / 246.6 | 174 | intergenic (‑8/‑78) | soxS/soxR | superoxide response regulon transcriptional activator; autoregulator/redox‑sensitive transcriptional activator of soxS; autorepressor |
| * | NC_000913 | 730,388 | 0 | A | T | 33.3% | 20.2 / 13.6 | 18 | E269V (GAA→GTA) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 730,389 | 0 | A | T | 33.3% | 20.6 / 13.7 | 18 | E269D (GAA→GAT) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.0% | 448.7 / 154.8 | 261 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,674,958 | 0 | A | T | 24.0% | 249.2 / 82.8 | 129 | intergenic (+11/+14) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 1,311,831 | 0 | C | T | 23.3% | 247.0 / 71.3 | 133 | intergenic (+23/+17) | tonB/yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| * | NC_000913 | 1,674,955 | 0 | A | T | 23.3% | 258.6 / 82.8 | 132 | intergenic (+8/+17) | tqsA/pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| * | NC_000913 | 3,439,588 | 0 | G | C | 22.9% | 369.6 / 115.6 | 176 | intergenic (‑79/+28) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913 | 1,311,830 | 0 | A | G | 22.7% | 240.8 / 72.4 | 135 | intergenic (+22/+18) | tonB/yciA | membrane spanning protein in TonB‑ExbB‑ExbD transport complex/acyl‑CoA esterase |
| * | NC_000913 | 314,258 | 0 | G | A | 22.7% | 342.1 / 91.5 | 173 | intergenic (‑453/‑99) | ykgP/eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified |
| * | NC_000913 | 2,081,688 | 0 | A | T | 22.6% | 225.5 / 69.2 | 116 | I287N (ATT→AAT) | dacD | D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6b |
| * | NC_000913 | 314,255 | 0 | T | C | 22.4% | 317.8 / 92.5 | 172 | intergenic (‑450/‑102) | ykgP/eaeH | pseudogene, oxidoreductase family/pseudogene, attaching and effacing protein homology;factor; Not classified |
| * | NC_000913 | 569,160 | 0 | G | T | 22.0% | 446.1 / 92.8 | 191 | D87Y (GAC→TAC) | ybcK | DLP12 prophage; putative recombinase |
| * | NC_000913 | 1,406,098 | 0 | C | T | 22.0% | 280.1 / 71.1 | 141 | D40D (GAC→GAT) | smrA | DNA endonuclease |
| * | NC_000913 | 4,060,264 | 0 | A | C | 21.9% | 261.2 / 99.8 | 165 | intergenic (+34/‑183) | typA/yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 1,224,239 | 0 | A | T | 21.9% | 270.5 / 72.8 | 129 | intergenic (+332/+40) | ycgI/minE | pseudogene/cell division topological specificity factor |
| * | NC_000913 | 3,439,589 | 0 | G | C | 21.7% | 406.6 / 114.8 | 185 | intergenic (‑80/+27) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913 | 3,810,324 | 0 | G | A | 21.5% | 292.1 / 72.0 | 148 | intergenic (+20/+19) | coaD/mutM | pantetheine‑phosphate adenylyltransferase/formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase |
| Marginal new junction evidence (lowest skew 10 of 1576 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 92 (1.240) +44 bp |
11/108 | 7.0 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 275007 | NA (NA) | 70 (0.540) | 18/190 | 9.2 | NA | noncoding (143/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 275025 | NA (NA) | noncoding (125/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 419210 = | 126 (0.940) | 22 (0.180) | 16/178 | 9.4 | 16.1% | intergenic (+26/‑381) | phoR/brnQ | sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| ? | NC_000913 | 419234 = | 115 (0.940) | intergenic (+50/‑357) | phoR/brnQ | sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val | |||||
| * | ? | NC_000913 | 4029696 = | 159 (1.180) | 21 (0.170) | 16/182 | 9.6 | 12.5% | coding (1276/2190 nt) | fadB | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| ? | NC_000913 | 4029719 = | 146 (1.170) | coding (1253/2190 nt) | fadB | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase | |||||
| * | ? | NC_000913 | 228016 = | NA (NA) | 61 (0.490) | 16/182 | 9.6 | 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 | 274620 = | NA (NA) | 46 (0.380) | 15/178 | 9.8 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2430865 = | 148 (1.100) | 19 (0.220) +35 bp |
8/126 | 9.9 | 16.7% | intergenic (‑102/+157) | cvpA/dedD | colicin V production protein/membrane‑anchored periplasmic protein involved in septation |
| ? | NC_000913 | = 3297083 | NA (NA) | intergenic (+99/+15) | yraP/yraQ | outer membrane lipoprotein/putative inner membrane permease | |||||
| * | ? | NC_000913 | 232549 = | 139 (1.030) | 21 (0.170) | 15/180 | 9.9 | 14.6% | coding (624/624 nt) | yafE | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | 232587 = | 117 (0.950) | intergenic (+38/+10) | yafE/mltD | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase/putative membrane‑bound lytic murein transglycosylase D | |||||
| * | ? | NC_000913 | = 225998 | NA (NA) | 37 (0.290) | 16/188 | 9.9 | NA | noncoding (240/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 226015 | NA (NA) | noncoding (257/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 224059 = | NA (NA) | 53 (0.420) | 15/182 | 10.0 | 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 | |||||