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 33 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,684,779 | 0 | A | C | 45.6% | 38.2 / 12.0 | 50 | G243G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| * | NC_000913 | 3,745,019 | 0 | C | G | 38.7% | 38.5 / 10.1 | 31 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,745,397 | 0 | A | C | 36.4% | 95.8 / 11.2 | 57 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 433,649 | 0 | T | G | 36.0% | 55.3 / 17.8 | 77 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 31.8% | 126.7 / 33.2 | 63 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| * | NC_000913 | 1,265,473 | 0 | T | G | 31.3% | 152.8 / 12.7 | 67 | G154G (GGT→GGG) | prfA | peptide chain release factor RF‑1 |
| * | NC_000913 | 825,235 | 0 | T | A | 30.5% | 76.8 / 21.5 | 61 | M292L (ATG→TTG) | ybhR | putative ABC transporter permease |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.3% | 298.2 / 151.7 | 184 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 433,634 | 0 | T | G | 27.6% | 104.6 / 21.2 | 89 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 1,563,399 | 0 | A | G | 26.4% | 207.8 / 14.9 | 91 | S779P (TCC→CCC) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| * | NC_000913 | 540,558 | 0 | T | G | 26.1% | 194.6 / 19.1 | 88 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 1,513,995 | 0 | A | G | 25.8% | 200.1 / 20.0 | 93 | G55G (GGA→GGG) | ydcU | putative ABC transporter permease |
| * | NC_000913 | 954,388 | 0 | C | T | 25.0% | 79.3 / 12.2 | 57 | A27T (GCA→ACA) | focA | formate channel |
| * | NC_000913 | 4,101,514 | 0 | G | T | 25.0% | 117.5 / 12.0 | 49 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 4,449,045 | 0 | T | G | 24.4% | 200.9 / 14.4 | 90 | intergenic (+3/+77) | chpB/ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| * | NC_000913 | 422,218 | 0 | C | T | 23.4% | 164.1 / 14.7 | 79 | F411F (TTC→TTT) | proY | proline‑specific permease |
| * | NC_000913 | 4,548,932 | 0 | A | T | 23.1% | 120.1 / 10.5 | 52 | Y42F (TAT→TTT) | fimH | minor component of type 1 fimbriae |
| * | NC_000913 | 1,825,130 | 0 | G | T | 22.9% | 143.8 / 11.3 | 70 | intergenic (‑193/+10) | ves/spy | cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| * | NC_000913 | 1,984,158 | 0 | G | C | 22.2% | 216.7 / 15.6 | 90 | G304G (GGC→GGG) | araG | L‑arabinose ABC transporter ATPase |
| * | NC_000913 | 3,595,316 | 0 | G | A | 21.8% | 85.7 / 12.3 | 59 | V55V (GTC→GTT) | livM | branched‑chain amino acid ABC transporter permease |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225456 = | 72 (0.500) | 12 (0.090) | 11/314 | 5.5 | 15.0% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 3427056 | NA (NA) | intergenic (‑23/+20) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 225456 = | 72 (0.500) | 12 (0.090) | 11/314 | 5.5 | 13.5% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | 225477 = | 86 (0.640) | intergenic (+20/‑23) | ileV/alaV | tRNA‑Ile/tRNA‑Ala | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.050) | 6/280 | 6.7 | 4.7% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 121 (1.000) | intergenic (+175/+107) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 11 (0.080) | 7/314 | 6.8 | 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 | 1070548 = | 140 (0.980) | 7 (0.050) | 7/318 | 6.8 | 5.1% | coding (408/591 nt) | rutE | putative malonic semialdehyde reductase |
| ? | NC_000913 | 1070576 = | 127 (0.930) | coding (380/591 nt) | rutE | putative malonic semialdehyde reductase | |||||
| * | ? | NC_000913 | 225468 = | 86 (0.600) | 11 (0.080) | 7/314 | 6.8 | 11.9% | 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 = | 72 (0.500) | 11 (0.090) +22 bp |
6/288 | 6.8 | 11.1% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518117 | 131 (0.910) | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala | |||||
| * | ? | NC_000913 | 225456 = | 72 (0.500) | 10 (0.080) +23 bp |
5/286 | 7.2 | 10.8% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518231 | 121 (0.840) | noncoding (1/76 nt) | alaW | tRNA‑Ala | |||||
| * | ? | NC_000913 | = 1757687 | 214 (1.490) | 5 (0.040) | 5/304 | 7.4 | 2.4% | intergenic (+30/+34) | lpp/ldtE | murein lipoprotein/murein L,D‑transpeptidase |
| ? | NC_000913 | = 1757688 | 212 (1.620) | intergenic (+31/+33) | lpp/ldtE | murein lipoprotein/murein L,D‑transpeptidase | |||||
| * | ? | NC_000913 | 3515982 = | 164 (1.150) | 5 (0.040) | 5/314 | 7.5 | 3.2% | intergenic (‑69/+38) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| ? | NC_000913 | 3516010 = | 145 (1.070) | intergenic (‑97/+10) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring | |||||