mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 963 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,665,702 | 0 | C | A | 63.5% | 3.2 / 108.0 | 107 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 993,917 | 0 | A | C | 58.3% | 51.1 / 76.1 | 60 | V43G (GTG→GGG) | ssuB | aliphatic sulfonate ABC transporter ATPase |
| * | NC_000913 | 2,386,862 | 0 | G | A | 57.0% | ‑4.3 / 98.0 | 81 | intergenic (+31/‑72) | yfbL/yfbM | putative M28A family peptidase/DUF1877 family protein |
| * | NC_000913 | 3,665,698 | 0 | T | C | 55.3% | 17.4 / 114.6 | 104 | D38G (GAT→GGT) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 2,332,823 | 0 | A | G | 54.7% | 50.1 / 91.8 | 77 | pseudogene (1580/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| * | NC_000913 | 993,913 | 0 | G | C | 52.2% | 66.2 / 114.4 | 67 | G44G (GGC→GGG) | ssuB | aliphatic sulfonate ABC transporter ATPase |
| * | NC_000913 | 1,826,379 | 0 | T | C | 51.8% | 58.5 / 108.9 | 81 | E182G (GAG→GGG) | astE | succinylglutamate desuccinylase |
| * | NC_000913 | 357,890 | 0 | C | A | 50.0% | 10.9 / 26.5 | 36 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 2,337,723 | 0 | A | C | 50.0% | 103.6 / 30.2 | 82 | G566G (GGT→GGG) | gyrA | DNA gyrase (type II topoisomerase), subunit A |
| * | NC_000913 | 3,133,302 | 0 | T | G | 48.1% | 78.1 / 35.4 | 82 | H219P (CAC→CCC) | yghS | putative ATP‑binding protein |
| * | NC_000913 | 3,443,277 | 0 | A | C | 48.0% | 101.4 / 29.7 | 76 | V274G (GTA→GGA) | secY | preprotein translocase membrane subunit |
| * | NC_000913 | 345,328 | 0 | C | A | 46.4% | 125.5 / 73.8 | 110 | intergenic (+337/‑76) | yahL/yahM | uncharacterized protein/uncharacterized protein |
| * | NC_000913 | 2,378,968 | 0 | C | T | 45.8% | 32.7 / 40.4 | 73 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| * | NC_000913 | 300,711 | 0 | G | C | 45.6% | 111.4 / 51.0 | 79 | P75R (CCG→CGG) | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | NC_000913 | 300,721 | 0 | G | T | 45.6% | 108.1 / 43.9 | 79 | Q72K (CAA→AAA) | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | NC_000913 | 2,826,462 | 0 | G | A | 45.1% | 60.6 / 38.3 | 71 | G24E (GGA→GAA) | srlE | glucitol/sorbitol‑specific enzyme IIB component of PTS |
| * | NC_000913 | 354,288 | 0 | T | G | 44.9% | 133.4 / 33.0 | 89 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 540,558 | 0 | T | G | 44.6% | 109.1 / 46.0 | 93 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 2,228,275 | 0 | T | C | 44.4% | 66.5 / 22.1 | 73 | pseudogene (335/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 3,813,272 | 0 | C | T | 44.2% | 58.6 / 42.2 | 87 | S181L (TCG→TTG) | dfp | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| Marginal new junction evidence (lowest skew 10 of 137 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381689 | NA (NA) | 14 (0.160) | 10/278 | 5.9 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4409174 = | NA (NA) | 10 (0.120) | 8/266 | 6.5 | 7.5% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409235 = | 123 (1.450) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 2518231 | 80 (0.850) | 8 (0.100) +23 bp |
7/250 | 6.5 | 10.6% | noncoding (1/76 nt) | alaW | tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | 225456 = | 11 (0.120) | 8 (0.100) +23 bp |
7/250 | 6.5 | 17.2% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518231 | 80 (0.850) | noncoding (1/76 nt) | alaW | tRNA‑Ala | |||||
| * | ? | NC_000913 | = 2518117 | 74 (0.780) | 8 (0.100) +22 bp |
7/252 | 6.6 | 11.3% | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | 225456 = | 11 (0.120) | 8 (0.100) +22 bp |
7/252 | 6.6 | 18.1% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518117 | 74 (0.780) | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala | |||||
| * | ? | NC_000913 | = 1987441 | 88 (0.930) | 8 (0.090) | 7/276 | 7.1 | 9.0% | intergenic (+13/+66) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein |
| ? | NC_000913 | = 1987450 | 79 (0.900) | intergenic (+22/+57) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 8 (0.090) | 7/278 | 7.2 | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 225468 = | 14 (0.150) | 8 (0.090) | 7/278 | 7.2 | 37.8% | intergenic (+11/‑32) | ileV/alaV | tRNA‑Ile/tRNA‑Ala |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 225456 = | 11 (0.120) | 8 (0.090) | 7/278 | 7.2 | 43.6% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 3427056 | NA (NA) | intergenic (‑23/+20) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||