mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 44 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 | 32.6% | 42.6 / 32.8 | 43 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 2,488,700 | 0 | G | A | 31.7% | 233.2 / 40.0 | 124 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 2,004,055 | 0 | A | C | 31.6% | 193.7 / 25.3 | 98 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 3,205,091 | 0 | C | T | 29.6% | 173.7 / 42.0 | 98 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 2,004,048 | 0 | G | A | 27.6% | 196.4 / 44.4 | 98 | intergenic (‑122/+199) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 3,475,533 | 0 | C | T | 27.3% | 270.0 / 45.8 | 132 | E10K (GAA→AAA) | fabR | HTH‑type transcriptional repressor FabR |
| * | NC_007779 | 1,826,775 | 0 | G | A | 27.2% | 212.6 / 24.7 | 92 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 4,609,024 | 0 | C | T | 26.6% | 217.8 / 36.4 | 109 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 3,895,373 | 0 | T | G | 26.6% | 112.9 / 14.8 | 65 | D80A (GAC→GCC) | yiaN | 2,3‑diketo‑L‑gulonate transporter large permease YiaN |
| * | NC_007779 | 1,826,770 | 0 | G | A | 25.6% | 196.6 / 26.2 | 82 | intergenic (‑119/+84) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 1,097,540 | 0 | C | A | 25.5% | 117.3 / 21.4 | 48 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,205,151 | 0 | G | A | 25.5% | 213.2 / 18.9 | 106 | V11V (GTG→GTA) | ttdA | L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 753,547 | 0 | T | A | 24.8% | 254.7 / 31.1 | 101 | intergenic (‑330/+60) | Y75_RS03720/gltA | type 1 fimbrial protein/citrate (Si)‑synthase |
| * | NC_007779 | 3,401,314 | 0 | T | C | 24.6% | 277.6 / 29.7 | 115 | D625G (GAT→GGT) | csrD | RNase E specificity factor CsrD |
| * | NC_007779 | 2,827,162 | 0 | T | G | 24.3% | 182.5 / 27.0 | 108 | V257G (GTG→GGG) | srlD | sorbitol‑6‑phosphate dehydrogenase |
| * | NC_007779 | 2,488,714 | 0 | T | A | 24.0% | 264.4 / 30.5 | 121 | L24F (TTA→TTT) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 2,902,342 | 0 | G | T | 24.0% | 268.3 / 14.7 | 97 | intergenic (+312/+1061) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 2,902,348 | 0 | C | A | 24.0% | 257.4 / 35.9 | 96 | intergenic (+318/+1055) | Y75_RS14470/queE | kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NC_007779 | 4,108,976 | 0 | T | G | 23.6% | 321.6 / 18.9 | 127 | Y334D (TAT→GAT) | Y75_RS20260 | DUF4153 domain‑containing protein |
| * | NC_007779 | 634,289 | 0 | C | A | 23.3% | 235.6 / 14.6 | 87 | G104V (GGT→GTT) | Y75_RS03120 | ParB‑like nuclease domain‑containing 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_007779 | 381401 = | NA (NA) | 80 (0.530) | 68/492 | 4.3 | 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) | 78 (0.510) | 68/496 | 4.4 | 96.3% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 3 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 2069490 | 167 (1.090) | 72 (0.470) | 16/496 | 18.3 | 45.9% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 3 (0.020) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 1413613 = | 174 (1.130) | 10 (0.070) | 9/444 | 20.7 | 6.8% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NC_007779 | = 1436672 | 120 (0.870) | intergenic (+39/+227) | Y75_RS24865/uspF | hypothetical protein/universal stress protein UspF | |||||
| * | ? | NC_007779 | 4547362 = | 159 (1.040) | 4 (0.030) | 4/478 | 25.8 | 2.6% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 146 (0.990) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 4610756 | 95 (0.620) | 4 (0.030) | 4/496 | 26.4 | 4.2% | intergenic (+36/+3) | Y75_RS22830/Y75_RS22835 | DUF1435 domain‑containing protein/tRNA‑Leu |
| ? | NC_007779 | 4610993 = | 87 (0.570) | intergenic (‑27/+2) | Y75_RS22840/Y75_RS22845 | tRNA‑Leu/tRNA‑Leu | |||||
| * | ? | NC_007779 | 1724330 = | 160 (1.040) | 3 (0.020) | 3/474 | 26.7 | 1.9% | coding (496/2013 nt) | Y75_RS08665 | FUSC family protein |
| ? | NC_007779 | = 1724326 | 152 (1.040) | coding (492/2013 nt) | Y75_RS08665 | FUSC family protein | |||||
| * | ? | NC_007779 | = 4547370 | 164 (1.070) | 3 (0.020) | 3/478 | 26.8 | 1.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 145 (0.980) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||