mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 117 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,634,946 | 0 | G | T | 29.2% | 53.3 / 14.8 | 24 | A301D (GCT→GAT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 1,634,949 | 0 | G | C | 29.2% | 52.9 / 18.2 | 24 | A300G (GCT→GGT) | stfQ | Qin prophage; putative side tail fibre assembly protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.4% | 390.3 / 164.5 | 235 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,291,513 | 0 | T | C | 25.9% | 252.6 / 102.6 | 148 | M1A (GTG→GCG) †‡ | nrfE | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| * | NC_000913 | 4,291,512 | 0 | G | A | 25.7% | 265.1 / 100.9 | 148 | M1M (GTG→ATG) †‡ | nrfE | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| * | NC_000913 | 2,089,854 | 0 | A | T | 25.2% | 208.4 / 74.2 | 107 | intergenic (‑141/‑142) | yefM/hisL | antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide |
| * | NC_000913 | 1,015,912 | 0 | T | A | 24.5% | 290.3 / 103.2 | 147 | intergenic (+30/+40) | rmf/fabA | ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase |
| * | NC_000913 | 3,439,588 | 0 | G | C | 24.2% | 329.7 / 121.0 | 158 | intergenic (‑79/+28) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913 | 2,286,142 | 0 | T | A | 23.9% | 277.4 / 92.7 | 135 | intergenic (+6/‑69) | yejM/proL | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro |
| * | NC_000913 | 3,057,140 | 0 | A | G | 23.8% | 243.6 / 76.2 | 126 | intergenic (+152/+38) | sibC/serA | sRNA antisense regulator of toxic IbsC protein/D‑3‑phosphoglycerate dehydrogenase |
| * | NC_000913 | 2,519,222 | 0 | T | G | 23.6% | 263.9 / 87.8 | 123 | intergenic (+17/+35) | yfeD/gltX | DUF1323 family putative DNA‑binding protein/glutamyl‑tRNA synthetase |
| * | NC_000913 | 252,589 | 0 | G | C | 23.5% | 293.6 / 99.5 | 136 | A97P (GCA→CCA) | yafO | mRNA interferase toxin of the YafO‑YafN toxin‑antitoxin system |
| * | NC_000913 | 2,286,139 | 0 | A | T | 23.4% | 290.2 / 87.4 | 137 | intergenic (+3/‑72) | yejM/proL | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro |
| * | NC_000913 | 4,262,250 | 0 | G | C | 23.3% | 326.0 / 108.1 | 150 | G194G (GGG→GGC) | dusA | tRNA‑dihydrouridine synthase A |
| * | NC_000913 | 3,439,589 | 0 | G | C | 23.3% | 357.1 / 119.5 | 163 | intergenic (‑80/+27) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913 | 1,406,093 | 0 | A | G | 23.3% | 194.0 / 61.8 | 103 | I39V (ATC→GTC) | smrA | DNA endonuclease |
| * | NC_000913 | 595,519 | 0 | T | A | 23.2% | 281.6 / 91.9 | 139 | intergenic (‑76/‑81) | cusR/cusC | response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component |
| * | NC_000913 | 1,850,719 | 1 | . | T | 23.2% | 224.0 / 96.2 | 95 | intergenic (+26/‑141) | sppA/ansA | protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1 |
| * | NC_000913 | 3,183,345 | 1 | . | T | 23.1% | 334.5 / 133.5 | 130 | intergenic (+22/+468) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| * | NC_000913 | 3,657,603 | 0 | T | A | 23.1% | 324.6 / 99.1 | 156 | intergenic (+36/+383) | hdeD/arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| Marginal new junction evidence (lowest skew 10 of 1312 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1468681 | NA (NA) | 87 (1.270) +44 bp |
11/110 | 6.3 | NA | noncoding (560/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1650843 = | NA (NA) | noncoding (1/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4171607 | 29 (0.230) | 55 (0.470) | 18/186 | 8.3 | 66.9% | intergenic (+63/‑30) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon |
| ? | NC_000913 | = 4213022 | NA (NA) | intergenic (+76/‑18) | rrlE/rrfE | 23S ribosomal RNA of rrnE operon/5S ribosomal RNA of rrnE operon | |||||
| * | ? | NC_000913 | = 3944978 | NA (NA) | 72 (0.620) | 16/186 | 9.0 | 81.0% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4038811 | 18 (0.150) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 53 (0.460) | 16/186 | 9.0 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 225685 | 131 (1.060) | 49 (0.420) | 16/186 | 9.0 | 28.5% | intergenic (+110/‑74) | alaV/rrlH | tRNA‑Ala/23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 3943636 | NA (NA) | intergenic (+126/‑68) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | = 2917925 | 143 (1.150) | 20 (0.250) +35 bp |
8/128 | 9.2 | 17.9% | noncoding (38/95 nt) | RIP202 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP202 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 3706060 | NA (NA) | noncoding (98/98 nt) | RIP266 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP266 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 224059 = | NA (NA) | 62 (0.540) | 15/184 | 9.3 | NA | noncoding (289/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 224082 = | NA (NA) | noncoding (312/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 4040481 | NA (NA) | 31 (0.270) | 15/186 | 9.4 | 100% | intergenic (+58/‑36) | rrlA/rrfA | 23S ribosomal RNA of rrnA operon/5S ribosomal RNA of rrnA operon |
| ? | NC_000913 | = 4040505 | 0 (0.000) | intergenic (+82/‑12) | rrlA/rrfA | 23S ribosomal RNA of rrnA operon/5S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 3946688 | 129 (1.040) | 52 (0.450) | 15/186 | 9.4 | 30.0% | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4171601 | NA (NA) | intergenic (+57/‑36) | rrlB/rrfB | 23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon | |||||
| * | ? | NC_000913 | 2727891 = | NA (NA) | 70 (0.600) | 15/186 | 9.4 | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||