mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 31 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,166,856 | 0 | G | A | 50.0% | 6.6 / 67.8 | 46 | noncoding (198/1542 nt) | rrsB | 16S ribosomal RNA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 39.0% | 225.0 / 24.2 | 146 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,401,345 | 0 | G | T | 33.0% | 173.2 / 10.1 | 109 | intergenic (‑258/+47) | mreB/csrD | dynamic cytoskeletal protein MreB/regulator of CsrB and CsrC decay |
| * | NC_000913 | 2,472,817 | 0 | C | A | 32.2% | 129.5 / 14.0 | 87 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 1,272,420 | 0 | C | A | 31.9% | 188.2 / 28.9 | 113 | intergenic (+71/‑87) | chaB/chaC | putative cation transport regulator ChaB/glutathione‑specific gamma‑glutamylcyclotransferase |
| * | NC_000913 | 2,990,480 | 0 | C | A | 30.3% | 211.2 / 10.8 | 122 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,054,886 | 0 | G | T | 29.3% | 150.9 / 21.1 | 92 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,543,085 | 0 | C | A | 28.8% | 232.4 / 11.5 | 126 | intergenic (+121/‑82) | feoC/rpnA | ferrous iron transport protein FeoC/recombination‑promoting nuclease RpnA |
| * | NC_000913 | 2,427,716 | 0 | C | A | 28.7% | 257.3 / 11.9 | 122 | E26* (GAG→TAG) | argT | lysine/arginine/ornithine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,756,353 | 0 | C | A | 28.6% | 217.3 / 12.1 | 119 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 1,246,568 | 0 | C | A | 28.4% | 145.8 / 12.0 | 88 | W270L (TGG→TTG) | treA | periplasmic trehalase |
| * | NC_000913 | 710,830 | 0 | G | T | 28.4% | 227.8 / 18.0 | 134 | intergenic (‑105/+105) | uof/fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.1% | 219.3 / 17.2 | 128 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 377,402 | 0 | G | A | 27.4% | 150.2 / 53.5 | 85 | intergenic (+91/+133) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 377,407 | 0 | C | T | 27.4% | 150.0 / 59.5 | 84 | intergenic (+96/+128) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 3,269,935 | 0 | A | C | 27.3% | 132.7 / 10.1 | 99 | intergenic (+333/+281) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 4,296,191 | 0 | A | C | 26.9% | 31.8 / 10.1 | 26 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 847,955 | 0 | G | A | 25.6% | 250.9 / 50.2 | 156 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,054,894 | 0 | G | T | 25.3% | 138.5 / 12.2 | 79 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,470,627 | 0 | C | A | 25.2% | 283.4 / 11.3 | 127 | pseudogene (109/3495 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 366180 | 1187 (12.210) | 79 (0.810) | 49/588 | 0.6 | 11.8% | coding (126/3075 nt) | lacZ | beta‑galactosidase |
| ? | NC_000913 | 366274 = | 0 (0.000) | coding (32/3075 nt) | lacZ | beta‑galactosidase | |||||
| * | ? | NC_000913 | = 3648146 | 105 (1.080) | 11 (0.140) | 11/472 | 4.3 | 10.5% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 104 (1.330) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 366907 = | 4562 (46.920) | 18 (0.190) | 14/570 | 4.4 | 0.41% | coding (604/1083 nt) | lacI | DNA‑binding transcriptional repressor LacI |
| ? | NC_000913 | = 366910 | 4422 (46.920) | coding (601/1083 nt) | lacI | DNA‑binding transcriptional repressor LacI | |||||
| * | ? | NC_000913 | = 781222 | 64 (0.660) | 8 (0.110) | 7/436 | 5.3 | 15.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 40 (0.560) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 2357730 | 102 (1.050) | 8 (0.100) | 8/508 | 5.6 | 8.9% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 75 (0.890) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 2518116 | 70 (0.720) | 4 (0.060) | 4/426 | 6.6 | 8.2% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 39 (0.550) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 781322 | 59 (0.610) | 8 (0.090) | 5/510 | 6.9 | 11.5% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 72 (0.850) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 780918 | 77 (0.790) | 5 (0.070) | 3/436 | 7.3 | 9.4% | noncoding (76/76 nt) | lysW | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 39 (0.540) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 4171849 | 58 (0.600) | 12 (0.130) +CTCTAGC |
5/574 | 7.5 | 15.2% | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase |
| ? | NC_000913 | 4171930 = | 79 (0.810) | intergenic (+174/‑127) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase | |||||
| * | ? | NC_000913 | = 365734 | 4608 (47.400) | 5 (0.050) | 5/570 | 7.5 | 0.15% | coding (572/3075 nt) | lacZ | beta‑galactosidase |
| ? | NC_000913 | 366085 = | 2402 (25.490) | coding (221/3075 nt) | lacZ | beta‑galactosidase | |||||