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 58 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,099,404 | 0 | G | T | 74.0% | 125.1 / 58.5 | 73 | V176L (GTA→TTA) | ycdX | zinc‑binding phosphatase YcdX |
| * | NC_000913 | 2,726,996 | 0 | A | . | 70.0% | ‑6.8 / 10.3 | 10 | noncoding (2189/2904 nt) | rrlG | 23S ribosomal RNA |
| * | NC_000913 | 3,046,068 | 0 | T | A | 58.8% | 9.1 / 31.2 | 34 | intergenic (‑167/+100) | ygfF/gcvP | putative oxidoreductase YgfF/glycine decarboxylase |
| * | NC_000913 | 2,726,555 | 0 | C | A | 55.6% | ‑4.2 / 23.5 | 18 | noncoding (2630/2904 nt) | rrlG | 23S ribosomal RNA |
| * | NC_000913 | 2,726,560 | 0 | C | T | 55.6% | ‑4.2 / 20.4 | 18 | noncoding (2625/2904 nt) | rrlG | 23S ribosomal RNA |
| * | NC_000913 | 164,569 | 0 | C | G | 52.9% | 0.9 / 15.0 | 17 | intergenic (+35/‑161) | hrpB/mrcB | RNA‑dependent NTPase HrpB/peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| * | NC_000913 | 2,726,652 | 0 | A | G | 50.0% | ‑4.5 / 27.0 | 20 | noncoding (2533/2904 nt) | rrlG | 23S ribosomal RNA |
| * | NC_000913 | 4,209,602 | 0 | A | G | 46.2% | 7.8 / 13.7 | 13 | noncoding (1456/1542 nt) | rrsE | 16S ribosomal RNA |
| * | NC_000913 | 4,209,605 | 0 | G | A | 46.2% | 7.8 / 12.9 | 13 | noncoding (1459/1542 nt) | rrsE | 16S ribosomal RNA |
| * | NC_000913 | 224,771 | 0 | C | G | 40.0% | 1105.4 / inf | 707 | noncoding (1001/1542 nt) | rrsH | 16S ribosomal RNA |
| * | NC_000913 | 4,412,781 | 0 | C | G | 35.4% | 86.7 / 12.4 | 52 | S132C (TCT→TGT) | yjfM | DUF1190 domain‑containing protein YjfM |
| * | NC_000913 | 4,209,608 | 0 | C | G | 35.3% | 23.6 / 16.8 | 17 | noncoding (1462/1542 nt) | rrsE | 16S ribosomal RNA |
| * | NC_000913 | 361,311 | 0 | C | A | 35.0% | 151.3 / 18.8 | 106 | E184* (GAA→TAA) | lacA | galactoside O‑acetyltransferase |
| * | NC_000913 | 4,038,738 | 0 | C | T | 34.5% | 656.6 / inf | 336 | noncoding (1220/2905 nt) | rrlA | 23S ribosomal RNA |
| * | NC_000913 | 4,038,805 | 0 | G | A | 32.5% | 276.9 / 147.4 | 163 | noncoding (1287/2905 nt) | rrlA | 23S ribosomal RNA |
| * | NC_000913 | 2,730,894 | 0 | G | C | 30.6% | 771.2 / inf | 341 | noncoding (264/1542 nt) | rrsG | 16S ribosomal RNA |
| * | NC_000913 | 361,320 | 0 | C | A | 30.2% | 165.3 / 20.2 | 106 | V181F (GTT→TTT) | lacA | galactoside O‑acetyltransferase |
| * | NC_000913 | 4,038,781 | 0 | A | G | 29.9% | 469.1 / 201.3 | 235 | noncoding (1263/2905 nt) | rrlA | 23S ribosomal RNA |
| * | NC_000913 | 2,730,900 | 0 | C | T | 28.8% | 783.7 / 293.3 | 358 | noncoding (258/1542 nt) | rrsG | 16S ribosomal RNA |
| * | NC_000913 | 2,730,908 | 0 | A | T | 28.4% | 844.3 / inf | 371 | noncoding (250/1542 nt) | rrsG | 16S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 93 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 96 (0.880) | 21 (0.220) | 13/248 | 2.1 | 17.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 114 (1.190) | intergenic (‑483/‑83) | tfaE/pinE | e14 prophage; putative tail fiber assembly protein TfaE/e14 prophage; site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 4175464 | 121 (1.110) | 12 (0.180) +55 bp |
5/170 | 2.9 | 14.1% | intergenic (+1/‑8) | thrU/tyrU | tRNA‑Thr/tRNA‑Tyr |
| ? | NC_000913 | 4175475 = | 122 (1.120) | noncoding (4/85 nt) | tyrU | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 374922 = | 142 (1.310) | 13 (0.160) | 7/206 | 2.9 | 12.3% | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | 81 (1.020) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 1286708 = | 178 (1.640) | 13 (0.140) | 8/238 | 3.0 | 4.8% | intergenic (+182/‑1) | narI/ychS | nitrate reductase A subunit gamma/putative uncharacterized protein YchS |
| ? | NC_000913 | = 1287241 | 363 (3.940) | intergenic (‑5/+3) | rttR/tyrV | small RNA RttR/tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 374963 | 144 (1.330) | 21 (0.280) | 6/194 | 3.0 | 17.1% | intergenic (+82/‑496) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | = 377487 | 104 (1.390) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 340006 | 59 (0.550) | 18 (0.210) +29 bp |
6/220 | 3.3 | 21.5% | coding (238/321 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | = 377529 | 107 (0.990) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375124 = | 172 (1.580) | 8 (0.110) | 4/196 | 3.7 | 6.7% | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | 104 (1.370) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 339820 | 70 (0.650) | 14 (0.160) +29 bp |
5/220 | 3.7 | 16.6% | coding (52/321 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | = 377529 | 107 (0.990) | intergenic (+218/+6) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3589065 = | 97 (0.890) | 8 (0.080) | 6/260 | 3.8 | 5.6% | coding (116/1071 nt) | ugpC | sn‑glycerol 3‑phosphate ABC transporter ATP binding subunit |
| ? | NC_000913 | = 3908232 | 178 (1.770) | coding (135/774 nt) | pstB | phosphate ABC transporter ATP binding subunit | |||||
| * | ? | NC_000913 | = 2304959 | 54 (0.500) | 7 (0.080) | 5/238 | 3.9 | 9.2% | intergenic (+566/+149) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | = 4325900 | 93 (1.010) | intergenic (‑159/+499) | yjdN/yjdM | PF06983 family protein YjdN/zinc ribbon domain‑containing protein YjdM | |||||