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 69 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 1,097,580 | 0 | C | T | 32.4% | 127.9 / 93.7 | 105 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,895,018 | 0 | T | G | 29.4% | 94.0 / 13.9 | 68 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate transporter large permease YiaN |
| * | NC_007779 | 753,547 | 0 | T | A | 28.6% | 383.2 / 66.5 | 168 | intergenic (‑330/+60) | Y75_RS03720/gltA | type 1 fimbrial protein/citrate (Si)‑synthase |
| * | NC_007779 | 3,205,091 | 0 | C | T | 28.5% | 274.8 / 54.2 | 144 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 2,004,055 | 0 | A | C | 27.8% | 352.7 / 29.5 | 151 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 4,108,976 | 0 | T | G | 26.9% | 531.6 / 19.8 | 217 | Y334D (TAT→GAT) | Y75_RS20260 | DUF4153 domain‑containing protein |
| * | NC_007779 | 4,609,024 | 0 | C | T | 26.8% | 287.9 / 44.6 | 142 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 2,902,348 | 0 | C | A | 26.5% | 438.4 / 67.4 | 167 | intergenic (+318/+1055) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 432,858 | 0 | T | G | 26.3% | 264.0 / 19.7 | 153 | G60G (GGT→GGG) | ribD | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase RibD |
| * | NC_007779 | 1,437,441 | 0 | G | A | 26.1% | 301.2 / 58.3 | 134 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 1,826,775 | 0 | G | A | 26.1% | 336.8 / 44.4 | 142 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 4,291,309 | 0 | T | A | 25.4% | 401.5 / 68.2 | 173 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 3,535,174 | 0 | A | C | 25.2% | 375.7 / 14.6 | 159 | intergenic (‑183/+77) | kdgT/sodA | 2‑keto‑3‑deoxygluconate transporter/superoxide dismutase [Mn] |
| * | NC_007779 | 4,585,314 | 0 | C | T | 25.0% | 400.2 / 37.0 | 164 | E277K (GAA→AAA) | hsdS | type I restriction‑modification system specificity subunit |
| * | NC_007779 | 3,475,533 | 0 | C | T | 24.6% | 392.3 / 57.4 | 179 | E10K (GAA→AAA) | fabR | HTH‑type transcriptional repressor FabR |
| * | NC_007779 | 2,983,387 | 0 | T | G | 24.6% | 238.7 / 17.9 | 117 | M288L (ATG→CTG) | Y75_RS14830 | acetyl‑CoA C‑acetyltransferase |
| * | NC_007779 | 3,176,404 | 0 | C | A | 24.4% | 387.0 / 49.1 | 164 | E55* (GAG→TAG) | nudF | ADP‑ribose diphosphatase |
| * | NC_007779 | 2,983,371 | 0 | A | T | 24.2% | 268.1 / 39.3 | 121 | V293E (GTG→GAG) | Y75_RS14830 | acetyl‑CoA C‑acetyltransferase |
| * | NC_007779 | 2,983,394 | 0 | C | G | 24.2% | 328.7 / 48.2 | 120 | P285P (CCG→CCC) | Y75_RS14830 | acetyl‑CoA C‑acetyltransferase |
| * | NC_007779 | 2,902,371 | 0 | G | A | 24.1% | 368.1 / 82.3 | 162 | intergenic (+341/+1032) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 381401 = | NA (NA) | 123 (0.580) | 105/492 | 3.6 | NA | coding (512/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381812 | NA (NA) | pseudogene (174/174 nt) | Y75_RS23175 | acetyltransferase | |||||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 126 (0.590) | 99/496 | 4.3 | 96.2% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 5 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 2069490 | 218 (1.030) | 115 (0.540) | 24/496 | 22.2 | 50.8% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 5 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 4610846 | 129 (0.610) | 9 (0.070) | 7/318 | 24.2 | 8.8% | intergenic (‑1/+34) | Y75_RS22835/Y75_RS22840 | tRNA‑Leu/tRNA‑Leu |
| ? | NC_007779 | 4611083 = | 104 (0.760) | intergenic (‑2/+266) | Y75_RS22845/rsmC | tRNA‑Leu/16S rRNA (guanine(1207)‑N(2))‑methyltransferase RsmC | |||||
| * | ? | NC_007779 | = 697163 | 154 (0.720) | 8 (0.060) | 8/340 | 24.6 | 6.7% | intergenic (‑1/+15) | Y75_RS03450/Y75_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NC_007779 | 697557 = | 118 (0.810) | intergenic (‑2/+378) | Y75_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NC_007779 | 1724330 = | 188 (0.880) | 3 (0.010) | 3/474 | 35.5 | 1.6% | coding (496/2013 nt) | Y75_RS08665 | FUSC family protein |
| ? | NC_007779 | = 1724326 | 184 (0.910) | coding (492/2013 nt) | Y75_RS08665 | FUSC family protein | |||||
| * | ? | NC_007779 | 2891334 = | 170 (0.800) | 3 (0.010) | 3/478 | 35.7 | 1.8% | coding (22/1272 nt) | Y75_RS14425 | FAD‑dependent oxidoreductase |
| ? | NC_007779 | = 2891330 | 167 (0.820) | coding (18/1272 nt) | Y75_RS14425 | FAD‑dependent oxidoreductase | |||||