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 53 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 289,922 | 0 | T | A | 57.5% | 185.6 / inf | 268 | pseudogene (649/698 nt) | Y75_RS01415 | IS1 family transposase |
| * | NC_007779 | 1,097,580 | 0 | C | T | 42.9% | 36.2 / 89.2 | 71 | intergenic (+329/+45) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,205,091 | 0 | C | T | 38.4% | 136.0 / 77.4 | 113 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 539,782 | 0 | T | G | 30.6% | 215.4 / 33.6 | 108 | intergenic (+50/‑7) | allB/Y75_RS02625 | allantoinase AllB/uracil/xanthine transporter |
| * | NC_007779 | 3,205,100 | 0 | T | A | 29.7% | 188.5 / 40.1 | 111 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 2,004,055 | 0 | A | C | 29.6% | 260.3 / 22.0 | 116 | intergenic (‑129/+192) | Y75_RS10125/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NC_007779 | 753,547 | 0 | T | A | 29.1% | 229.9 / 39.8 | 103 | intergenic (‑330/+60) | Y75_RS03720/gltA | type 1 fimbrial protein/citrate (Si)‑synthase |
| * | NC_007779 | 4,291,309 | 0 | T | A | 29.0% | 191.4 / 44.8 | 93 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NC_007779 | 3,404,073 | 0 | T | G | 28.3% | 253.7 / 13.4 | 113 | G245G (GGT→GGG) | Y75_RS16905 | oxidoreductase |
| * | NC_007779 | 3,205,102 | 0 | C | A | 28.2% | 180.2 / 31.9 | 110 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 1,826,775 | 0 | G | A | 27.4% | 206.8 / 33.3 | 95 | intergenic (‑124/+79) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 4,609,024 | 0 | C | T | 26.7% | 227.4 / 32.6 | 105 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NC_007779 | 1,826,770 | 0 | G | A | 25.6% | 201.8 / 30.1 | 90 | intergenic (‑119/+84) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone |
| * | NC_007779 | 3,404,070 | 0 | T | G | 25.2% | 262.3 / 13.6 | 116 | G244G (GGT→GGG) | Y75_RS16905 | oxidoreductase |
| * | NC_007779 | 1,097,540 | 0 | C | A | 25.0% | 130.8 / 35.4 | 64 | intergenic (+289/+85) | Y75_RS05375/Y75_RS05385 | hypothetical protein/RtT sRNA |
| * | NC_007779 | 3,205,108 | 0 | C | A | 24.7% | 218.8 / 32.7 | 98 | intergenic (‑196/‑11) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_007779 | 3,157,549 | 0 | T | C | 24.6% | 299.6 / 21.9 | 118 | intergenic (+9/+34) | yqhH/Y75_RS15695 | lipoprotein YqhH/YgiQ family radical SAM protein |
| * | NC_007779 | 29,496 | 0 | T | A | 24.5% | 271.5 / 34.3 | 106 | intergenic (+301/‑155) | dapB/Y75_RS00165 | 4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit |
| * | NC_007779 | 1,437,441 | 0 | G | A | 24.2% | 324.3 / 51.4 | 132 | intergenic (‑108/+33) | uspF/ompN | universal stress protein UspF/porin OmpN |
| * | NC_007779 | 3,004,668 | 0 | C | T | 23.8% | 303.9 / 32.8 | 130 | intergenic (‑226/‑253) | Y75_RS14955/ygeW | sigma‑54‑dependent transcriptional regulator/knotted carbamoyltransferase YgeW |
| 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 | 4310363 = | NA (NA) | 93 (0.600) | 79/496 | 3.0 | 98.9% | 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) | 58 (0.380) | 46/492 | 8.0 | 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 | = 2069490 | 167 (1.080) | 94 (0.610) | 23/496 | 14.9 | 52.8% | 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 | = 4610846 | 116 (0.750) | 7 (0.070) | 7/318 | 17.0 | 9.6% | intergenic (‑1/+34) | Y75_RS22835/Y75_RS22840 | tRNA‑Leu/tRNA‑Leu |
| ? | NC_007779 | 4611083 = | 58 (0.590) | intergenic (‑2/+266) | Y75_RS22845/rsmC | tRNA‑Leu/16S rRNA (guanine(1207)‑N(2))‑methyltransferase RsmC | |||||
| * | ? | NC_007779 | = 2946123 | 63 (0.410) | 5 (0.050) | 5/330 | 19.1 | 10.4% | intergenic (+4/‑30) | Y75_RS14670/Y75_RS14675 | tRNA‑Met/tRNA‑Met |
| ? | NC_007779 | 2946344 = | 44 (0.430) | intergenic (+5/+69) | Y75_RS14680/Y75_RS14685 | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NC_007779 | = 697163 | 102 (0.660) | 6 (0.060) | 5/340 | 19.5 | 7.0% | intergenic (‑1/+15) | Y75_RS03450/Y75_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NC_007779 | 697557 = | 89 (0.840) | intergenic (‑2/+378) | Y75_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NC_007779 | 1413613 = | 163 (1.060) | 5 (0.040) | 5/444 | 23.4 | 3.5% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NC_007779 | = 1436672 | 127 (0.920) | intergenic (+39/+227) | Y75_RS24865/uspF | hypothetical protein/universal stress protein UspF | |||||
| * | ? | NC_007779 | 3406257 = | 173 (1.120) | 4 (0.030) | 4/472 | 25.1 | 2.4% | coding (486/1350 nt) | accC | acetyl‑CoA carboxylase biotin carboxylase subunit |
| ? | NC_007779 | = 3406253 | 164 (1.120) | coding (482/1350 nt) | accC | acetyl‑CoA carboxylase biotin carboxylase subunit | |||||
| * | ? | NC_007779 | = 3497511 | 159 (1.030) | 3 (0.020) | 3/484 | 26.5 | 1.9% | coding (539/663 nt) | fsa | fructose‑6‑phosphate aldolase |
| ? | NC_007779 | = 3497526 | 157 (1.040) | coding (554/663 nt) | fsa | fructose‑6‑phosphate aldolase | |||||