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_007779 | 1,097,580 | 0 | C | T | 33.3% | 68.7 / 53.0 | 60 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 4,609,024 | 0 | C | T | 30.7% | 182.5 / 38.6 | 101 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 3,205,091 | 0 | C | T | 28.4% | 155.2 / 37.5 | 88 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 753,547 | 0 | T | A | 27.9% | 184.9 / 25.1 | 79 | intergenic (‑330/+60) | Y75_RS03720/gltA | type 1 fimbrial protein/citrate (Si)‑synthase |
| * | NC_007779 | 3,205,102 | 0 | C | A | 26.7% | 150.5 / 22.6 | 91 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 4,291,309 | 0 | T | A | 26.6% | 252.4 / 43.5 | 109 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 4,585,314 | 0 | C | T | 26.3% | 323.9 / 43.9 | 137 | E277K (GAA→AAA) | hsdS | type I restriction‑modification system specificity subunit |
| * | NC_007779 | 2,004,055 | 0 | A | C | 26.0% | 240.5 / 10.4 | 101 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 1,437,441 | 0 | G | A | 25.4% | 256.6 / 54.8 | 114 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 4,585,322 | 0 | G | T | 25.0% | 340.1 / 33.0 | 125 | S274* (TCA→TAA) | hsdS | type I restriction‑modification system specificity subunit |
| * | NC_007779 | 2,488,714 | 0 | T | A | 24.4% | 282.5 / 32.6 | 123 | L24F (TTA→TTT) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NC_007779 | 2,627,281 | 0 | A | C | 24.2% | 222.0 / 10.6 | 96 | V105G (GTC→GGC) | pdeF | cyclic‑guanylate‑specific phosphodiesterase PdeF |
| * | NC_007779 | 1,097,540 | 0 | C | A | 23.8% | 149.6 / 29.5 | 64 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,974,713 | 0 | G | T | 23.4% | 356.4 / 33.9 | 142 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NC_007779 | 3,157,549 | 0 | T | C | 22.9% | 272.9 / 22.5 | 105 | intergenic (+9/+34) | yqhH/Y75_RS15695 | lipoprotein YqhH/YgiQ family radical SAM protein |
| * | NC_007779 | 4,585,320 | 0 | C | T | 22.8% | 339.5 / 16.1 | 127 | E275K (GAA→AAA) | hsdS | type I restriction‑modification system specificity subunit |
| * | NC_007779 | 1,826,775 | 0 | G | A | 22.7% | 221.3 / 18.0 | 88 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 3,004,634 | 0 | C | A | 22.0% | 335.9 / 24.6 | 118 | intergenic (‑192/‑287) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| * | NC_007779 | 3,004,706 | 0 | G | A | 22.0% | 285.4 / 39.2 | 118 | intergenic (‑264/‑215) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| * | NC_007779 | 1,246,811 | 0 | G | T | 21.9% | 320.9 / 19.9 | 114 | L25F (TTG→TTT) | Y75_RS06255 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 105 (0.710) | 71/496 | 3.4 | 99.1% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 1 (0.010) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 381401 = | NA (NA) | 77 (0.530) | 63/492 | 4.4 | 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 | = 4547370 | 134 (0.910) | 18 (0.130) | 18/478 | 15.4 | 11.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 144 (1.010) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | 4547362 = | 135 (0.920) | 18 (0.130) | 18/478 | 15.4 | 11.6% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 144 (1.010) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2946123 | 43 (0.290) | 8 (0.080) | 8/330 | 15.8 | 16.4% | intergenic (+4/‑30) | Y75_RS14670/Y75_RS14675 | tRNA‑Met/tRNA‑Met |
| ? | NC_007779 | 2946344 = | 53 (0.540) | intergenic (+5/+69) | Y75_RS14680/Y75_RS14685 | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NC_007779 | = 697163 | 97 (0.660) | 7 (0.070) | 7/340 | 16.9 | 8.7% | intergenic (‑1/+15) | Y75_RS03450/Y75_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NC_007779 | 697557 = | 81 (0.800) | intergenic (‑2/+378) | Y75_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NC_007779 | = 2069490 | 173 (1.170) | 76 (0.520) | 15/496 | 17.4 | 46.6% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 1 (0.010) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 1413613 = | 157 (1.060) | 5 (0.040) | 5/444 | 22.2 | 3.2% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NC_007779 | = 1436672 | 160 (1.210) | intergenic (+39/+227) | Y75_RS24865/uspF | hypothetical protein/universal stress protein UspF | |||||
| * | ? | NC_007779 | 3406257 = | 161 (1.090) | 3 (0.020) | 3/472 | 24.9 | 1.9% | coding (486/1350 nt) | accC | acetyl‑CoA carboxylase biotin carboxylase subunit |
| ? | NC_007779 | = 3406253 | 153 (1.090) | coding (482/1350 nt) | accC | acetyl‑CoA carboxylase biotin carboxylase subunit | |||||
| * | ? | NC_007779 | = 2072408 | NA (NA) | 6 (0.040) | 3/492 | 25.5 | NA | intergenic (‑46/‑3) | Y75_RS10480/Y75_RS10490 | IS3‑like element IS2 family transposase/TonB‑dependent receptor plug domain‑containing protein |
| ? | NC_007779 | = 2105081 | NA (NA) | intergenic (‑33/+2) | Y75_RS10660/Y75_RS10665 | IS5‑like element IS5 family transposase/glycosyltransferase | |||||