mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 45.8% | 71.0 / 59.4 | 83 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 41.9% | 54.6 / 19.7 | 43 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 35.6% | 54.4 / 21.7 | 45 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.9% | 105.2 / 61.0 | 73 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 445,558 | 0 | A | C | 32.0% | 74.9 / 30.9 | 50 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,001,918 | 0 | A | C | 32.0% | 134.9 / 35.6 | 75 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.6% | 101.9 / 32.6 | 62 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.8% | 84.5 / 17.1 | 47 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.5% | 235.4 / 20.5 | 123 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,512,048 | 0 | A | C | 27.3% | 133.2 / 16.8 | 66 | L123V (TTG→GTG) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| * | NC_000913 | 1,068,173 | 0 | T | G | 25.0% | 214.0 / 21.0 | 92 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.1% | 123.2 / 17.6 | 58 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,565,621 | 0 | T | G | 23.8% | 168.2 / 13.2 | 80 | N38T (AAC→ACC) | dosP | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| * | NC_000913 | 4,429,984 | 0 | T | G | 23.3% | 210.7 / 19.0 | 86 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 22.9% | 133.2 / 19.5 | 48 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,679,688 | 0 | T | G | 22.9% | 190.2 / 15.9 | 83 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| * | NC_000913 | 1,550,663 | 0 | A | C | 22.8% | 132.7 / 12.7 | 57 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.4% | 165.7 / 25.9 | 70 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 20.4% | 408.4 / 21.1 | 162 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 646,747 | 0 | T | G | 20.3% | 158.2 / 20.4 | 64 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 119 (1.120) | 17 (0.180) | 16/246 | 3.9 | 15.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 87 (0.930) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 13 (0.150) | 6/226 | 6.5 | 12.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 93 (1.080) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 11 (0.110) | 6/258 | 7.2 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.060) | 5/262 | 7.8 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 72193 = | NA (NA) | 3 (0.030) | 3/226 | 8.1 | NA | noncoding (29/34 nt) | other | REP7b |
| ? | NC_000913 | = 4554510 | NA (NA) | noncoding (30/34 nt) | other | REP346 | |||||
| * | ? | NC_000913 | 4180665 = | 147 (1.390) | 4 (0.040) | 4/258 | 8.2 | 2.8% | coding (106/366 nt) | rplL | 50S ribosomal subunit protein L12 |
| ? | NC_000913 | = 4180661 | 139 (1.420) | coding (102/366 nt) | rplL | 50S ribosomal subunit protein L12 | |||||
| * | ? | NC_000913 | = 3067478 | 119 (1.120) | 4 (0.040) | 4/256 | 8.2 | 3.6% | coding (603/741 nt) | yggE | uncharacterized protein YggE |
| ? | NC_000913 | = 3067548 | 105 (1.080) | coding (533/741 nt) | yggE | uncharacterized protein YggE | |||||
| * | ? | NC_000913 | = 4461378 | 103 (0.970) | 4 (0.040) | 4/260 | 8.3 | 4.0% | coding (1283/2139 nt) | nrdD | anaerobic ribonucleoside‑triphosphate reductase |
| ? | NC_000913 | = 4461498 | 94 (0.950) | coding (1163/2139 nt) | nrdD | anaerobic ribonucleoside‑triphosphate reductase | |||||
| * | ? | NC_000913 | = 3058695 | 123 (1.160) | 4 (0.040) | 4/260 | 8.3 | 3.8% | coding (631/660 nt) | rpiA | ribose‑5‑phosphate isomerase A |
| ? | NC_000913 | = 3058850 | 85 (0.860) | coding (476/660 nt) | rpiA | ribose‑5‑phosphate isomerase A | |||||
| * | ? | NC_000913 | = 4436105 | 130 (1.230) | 3 (0.030) | 3/258 | 8.8 | 2.5% | coding (461/1944 nt) | cpdB | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| ? | NC_000913 | = 4436247 | 111 (1.130) | coding (319/1944 nt) | cpdB | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase | |||||