mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 970 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,206,435 | 0 | C | T | 50.8% | 77.0 / 186.6 | 118 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 357,890 | 0 | C | A | 48.7% | 47.7 / 60.3 | 78 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 689,514 | 0 | A | C | 47.0% | 141.9 / 23.8 | 100 | G456G (GGT→GGG) | lnt | apolipoprotein N‑acyltransferase |
| * | NC_000913 | 1,622,816 | 0 | G | A | 46.9% | 78.9 / 114.8 | 113 | intergenic (+75/+144) | yneM/dgcZ | inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing |
| * | NC_000913 | 2,326,450 | 0 | T | G | 45.9% | 190.8 / 18.0 | 110 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,601,176 | 0 | T | C | 44.4% | 113.8 / 60.3 | 100 | E304G (GAA→GGA) | ftsX | putative ABC transporter permease |
| * | NC_000913 | 3,350,853 | 0 | A | C | 44.1% | 204.8 / 28.2 | 127 | S725A (TCA→GCA) | arcB | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| * | NC_000913 | 29,496 | 0 | T | A | 43.8% | 153.5 / 64.9 | 113 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 599,576 | 0 | T | G | 43.4% | 165.6 / 45.7 | 100 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 29,486 | 0 | C | A | 42.9% | 166.9 / 68.8 | 112 | intergenic (+291/‑165) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 357,880 | 0 | T | C | 42.4% | 123.5 / 26.3 | 85 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 3,350,844 | 0 | A | C | 42.1% | 239.1 / 19.2 | 126 | L728V (TTA→GTA) | arcB | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| * | NC_000913 | 3,601,170 | 0 | G | C | 42.0% | 191.1 / 48.5 | 100 | A306G (GCA→GGA) | ftsX | putative ABC transporter permease |
| * | NC_000913 | 213,341 | 0 | A | G | 41.9% | 166.3 / 28.9 | 105 | G337G (GGA→GGG) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | NC_000913 | 266,349 | 0 | C | A | 41.7% | 225.4 / 53.3 | 115 | V69F (GTT→TTT) | yafY | lipoprotein, inner membrane; degP regulator; CP4‑6 prophage |
| * | NC_000913 | 17,050 | 0 | A | C | 41.7% | 183.2 / 12.8 | 108 | intergenic (‑90/‑439) | mokC/nhaA | regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter |
| * | NC_000913 | 3,947,831 | 0 | T | G | 41.2% | 164.8 / 25.8 | 98 | N46T (AAC→ACC) | hdfR | flhDC operon transcriptional repressor |
| * | NC_000913 | 3,443,277 | 0 | A | C | 41.0% | 228.5 / 26.6 | 118 | V274G (GTA→GGA) | secY | preprotein translocase membrane subunit |
| * | NC_000913 | 3,578,301 | 0 | A | C | 40.6% | 177.5 / 16.9 | 96 | G142G (GGT→GGG) | gntR | d‑gluconate inducible gluconate regulon transcriptional repressor |
| * | NC_000913 | 3,133,302 | 0 | T | G | 40.6% | 197.5 / 16.2 | 101 | H219P (CAC→CCC) | yghS | putative ATP‑binding protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 72 (0.570) | 60 (0.530) | 50/266 | 3.8 | 46.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 73 (0.650) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207790 = | 73 (0.580) | 39 (0.350) | 37/266 | 6.7 | 34.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 85 (0.750) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1209618 | 87 (0.690) | 55 (0.480) | 8/268 | 20.1 | 36.6% | pseudogene (2/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| ? | NC_000913 | 2471897 = | 112 (0.990) | pseudogene (226/579 nt) | yfdL | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3840542 = | 135 (1.070) | 6 (0.050) | 5/274 | 23.1 | 4.7% | intergenic (+34/+7) | yicS/nepI | putative periplasmic protein/putative transporter |
| ? | NC_000913 | 3840554 = | 119 (1.030) | coding (1186/1191 nt) | nepI | putative transporter | |||||
| * | ? | NC_000913 | 3399175 = | 144 (1.140) | 3 (0.030) | 3/280 | 25.5 | 2.2% | coding (804/1104 nt) | mreC | cell wall structural complex MreBCD transmembrane component MreC |
| ? | NC_000913 | = 3399171 | 134 (1.130) | coding (808/1104 nt) | mreC | cell wall structural complex MreBCD transmembrane component MreC | |||||