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 105 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,268 | 0 | T | C | 36.4% | 78.5 / 73.9 | 78 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 433,634 | 0 | T | G | 32.8% | 144.7 / 14.3 | 123 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.8% | 260.9 / 29.5 | 122 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,434,882 | 0 | T | G | 31.7% | 215.0 / 26.2 | 106 | Y252S (TAC→TCC) | truA | tRNA pseudouridine(38‑40) synthase |
| * | NC_000913 | 827,507 | 0 | T | G | 31.6% | 302.2 / 16.1 | 133 | D492A (GAC→GCC) | ybhF | ABC exporter ATP binding subunit YbhF |
| * | NC_000913 | 1,292,458 | 0 | T | A | 31.1% | 89.1 / 12.0 | 45 | intergenic (+93/+51) | galU/hns | UTP‑‑glucose‑1‑phosphate uridylyltransferase/DNA‑binding transcriptional dual regulator H‑NS |
| * | NC_000913 | 811,721 | 0 | T | G | 31.0% | 245.6 / 16.9 | 146 | V67G (GTG→GGG) | bioC | malonyl‑acyl carrier protein methyltransferase |
| * | NC_000913 | 786,855 | 0 | A | C | 30.5% | 280.0 / 15.8 | 118 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 2,185,199 | 0 | T | G | 30.5% | 359.0 / 39.0 | 175 | T35P (ACC→CCC) | thiM | hydroxyethylthiazole kinase |
| * | NC_000913 | 2,228,275 | 0 | T | C | 29.9% | 136.0 / 13.2 | 78 | intergenic (‑1005/‑707) | yohF/yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| * | NC_000913 | 4,256,069 | 0 | G | C | 29.9% | 163.8 / 22.9 | 77 | P133R (CCG→CGG) | plsB | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 28.8% | 386.1 / 13.8 | 158 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 4,457,105 | 0 | A | G | 28.7% | 303.3 / 27.7 | 139 | I441V (ATC→GTC) | mpl | UDP‑N‑acetylmuramate‑‑L‑alanyl‑gamma‑D‑glutamyl‑ meso‑2,6‑diaminoheptanedioate ligase |
| * | NC_000913 | 2,664,896 | 0 | T | G | 28.5% | 336.2 / 23.1 | 138 | G169G (GGT→GGG) | yfhR | putative peptidase |
| * | NC_000913 | 3,275,611 | 0 | A | C | 28.2% | 183.2 / 13.4 | 85 | E110D (GAA→GAC) | garD | GarD |
| * | NC_000913 | 4,056,115 | 0 | A | C | 28.2% | 275.3 / 18.3 | 119 | G75G (GGT→GGG) | glnL | protein histidine kinase NtrB |
| * | NC_000913 | 4,287,719 | 0 | T | A | 28.0% | 213.7 / 41.5 | 100 | intergenic (+52/‑45) | ytcB/nrfA | protein YtcB/cytochrome c552 nitrite reductase |
| * | NC_000913 | 1,015,516 | 0 | G | T | 27.8% | 158.3 / 15.9 | 72 | intergenic (+57/‑199) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| * | NC_000913 | 2,395,402 | 0 | A | C | 27.6% | 356.1 / 20.9 | 146 | G165G (GGT→GGG) | nuoJ | NADH:quinone oxidoreductase subunit J |
| * | NC_000913 | 2,745,089 | 0 | A | C | 27.3% | 296.3 / 21.6 | 122 | V84G (GTG→GGG) | trmD | tRNA m(1)G37 methyltransferase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1411899 = | 114 (0.900) | 5 (0.040) | 5/426 | 10.5 | 4.7% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 101 (0.890) | intergenic (‑552/+227) | ynaM/uspF | protein YnaM/universal stress protein F | |||||
| * | ? | NC_000913 | 4295832 = | 113 (0.890) | 3 (0.030) | 3/400 | 11.4 | 2.6% | intergenic (+38/+604) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | = 4296394 | 131 (1.230) | intergenic (+600/+42) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 2733016 | 160 (1.260) | 3 (0.020) | 3/478 | 12.5 | 1.9% | coding (714/2130 nt) coding (1158/2574 nt) |
clpB clpB |
chaperone protein ClpB chaperone protein ClpB |
| ? | NC_000913 | 3752913 = | 142 (1.120) | coding (922/975 nt) | yiaU | putative DNA‑binding transcriptional regulator YiaU | |||||
| * | ? | NC_000913 | = 1811315 | 151 (1.190) | 3 (0.020) +C |
3/476 | 12.5 | 2.0% | coding (382/1392 nt) | tcyP | cystine/sulfocysteine:cation symporter |
| ? | NC_000913 | = 4014805 | 138 (1.090) | coding (1753/2262 nt) | metE | cobalamin‑independent homocysteine transmethylase | |||||
| * | ? | NC_000913 | 1104384 = | 92 (0.730) | 3 (0.020) | 3/478 | 12.5 | 2.8% | coding (434/456 nt) | csgB | curlin, minor subunit |
| ? | NC_000913 | 1708463 = | 117 (0.920) | coding (1545/2223 nt) | rsxC | SoxR [2Fe‑2S] reducing system protein RsxC | |||||
| * | ? | NC_000913 | 898481 = | 90 (0.710) | 3 (0.020) | 3/478 | 12.5 | 2.4% | intergenic (+4/‑37) | ybjO/rlmC | putative inner membrane protein/23S rRNA m(5)U747 methyltransferase |
| ? | NC_000913 | = 3344179 | 149 (1.170) | coding (236/726 nt) | lptB | lipopolysaccharide transport system ATP binding protein LptB | |||||
| * | ? | NC_000913 | = 616210 | 149 (1.170) | 3 (0.020) +G |
3/476 | 12.5 | 2.1% | coding (2054/3882 nt) | entF | apo‑serine activating enzyme |
| ? | NC_000913 | = 1465821 | 137 (1.080) | pseudogene (430/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | = 447262 | 142 (1.120) | 3 (0.020) | 3/478 | 12.5 | 1.9% | coding (444/891 nt) | cyoE | heme O synthase |
| ? | NC_000913 | 3626058 = | 169 (1.330) | coding (746/1125 nt) | yhhJ | ABC transporter family protein YhhJ | |||||
| * | ? | NC_000913 | = 442737 | 142 (1.120) | 3 (0.020) | 3/478 | 12.5 | 2.1% | coding (1189/1449 nt) | thiI | tRNA uridine 4‑sulfurtransferase |
| ? | NC_000913 | 1263044 = | 134 (1.060) | coding (457/624 nt) | lolB | outer membrane lipoprotein LolB | |||||
| * | ? | NC_000913 | 418803 = | 141 (1.110) | 3 (0.020) | 3/478 | 12.5 | 2.0% | coding (915/1296 nt) | phoR | sensor histidine kinase PhoR |
| ? | NC_000913 | 2812840 = | 155 (1.220) | coding (225/1539 nt) | emrB | multidrug efflux pump membrane subunit EmrB | |||||