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 57 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,228,275 | 0 | T | C | 39.2% | 64.8 / 14.2 | 51 | intergenic (‑1005/‑707) | yohF/yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| * | NC_000913 | 811,721 | 0 | T | G | 35.9% | 148.7 / 21.0 | 108 | V67G (GTG→GGG) | bioC | malonyl‑acyl carrier protein methyltransferase |
| * | NC_000913 | 3,206,440 | 0 | C | A | 35.3% | 51.4 / 18.7 | 51 | intergenic (‑184/‑23) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,296,268 | 0 | T | C | 34.9% | 37.2 / 37.1 | 44 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,825,056 | 0 | G | A | 33.3% | 57.4 / 13.1 | 36 | intergenic (‑119/+84) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,762,308 | 0 | A | G | 32.4% | 111.0 / 11.3 | 75 | G42G (GGA→GGG) | rhsA | rhs element protein RhsA |
| * | NC_000913 | 433,649 | 0 | T | G | 31.8% | 77.0 / 13.7 | 89 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| * | NC_000913 | 1,764,774 | 0 | G | A | 31.1% | 79.5 / 12.1 | 45 | noncoding (7/68 nt) | rydB | small regulatory RNA RydB |
| * | NC_000913 | 2,962,495 | 0 | T | G | 30.9% | 126.5 / 14.5 | 86 | S90S (TCA→TCC) | ppdC | prepilin‑type N‑terminal cleavage/methylation domain‑containing protein PpdC |
| * | NC_000913 | 1,658,163 | 0 | C | T | 29.6% | 70.0 / 17.6 | 56 | S32F (TCT→TTT) | ynfE | putative selenate reductase YnfE |
| * | NC_000913 | 1,464,046 | 0 | G | T | 29.2% | 91.8 / 13.7 | 65 | E170* (GAA→TAA) | paaX | DNA‑binding transcriptional repressor PaaX |
| * | NC_000913 | 1,346,653 | 0 | C | A | 28.9% | 58.5 / 14.1 | 45 | L30F (TTG→TTT) | pdeR | cyclic di‑GMP phosphodiesterase PdeR |
| * | NC_000913 | 160,092 | 0 | C | A | 28.3% | 89.7 / 16.8 | 60 | L7F (TTG→TTT) | gluQ | glutamyl‑Q tRNA(Asp) synthetase |
| * | NC_000913 | 4,171,557 | 0 | C | G | 27.6% | 150.7 / 100.5 | 108 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA/5S ribosomal RNA |
| * | NC_000913 | 1,346,645 | 0 | G | A | 27.3% | 79.4 / 11.6 | 44 | S33F (TCT→TTT) | pdeR | cyclic di‑GMP phosphodiesterase PdeR |
| * | NC_000913 | 4,457,105 | 0 | A | G | 27.1% | 166.5 / 18.8 | 86 | I441V (ATC→GTC) | mpl | UDP‑N‑acetylmuramate‑‑L‑alanyl‑gamma‑D‑glutamyl‑ meso‑2,6‑diaminoheptanedioate ligase |
| * | NC_000913 | 3,203,329 | 0 | A | C | 27.0% | 151.5 / 14.7 | 101 | V268G (GTG→GGG) | bacA | undecaprenyl pyrophosphate phosphatase |
| * | NC_000913 | 1,328,465 | 0 | T | G | 26.0% | 136.0 / 12.0 | 77 | T216T (ACA→ACC) | yciK | putative oxidoreductase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.8% | 183.7 / 11.7 | 89 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 25.7% | 311.6 / 16.8 | 141 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4270388 = | 103 (1.050) | 3 (0.030) +G |
3/490 | 6.0 | 2.9% | coding (151/417 nt) | yjbQ | PF01894 family protein YjbQ |
| ? | NC_000913 | = 4339786 | 96 (0.980) | coding (736/2268 nt) | adiA | arginine decarboxylase, degradative | |||||
| * | ? | NC_000913 | = 3212126 | 121 (1.240) | 3 (0.030) | 3/490 | 6.0 | 2.3% | coding (1020/1746 nt) | dnaG | DNA primase |
| ? | NC_000913 | = 3851937 | 134 (1.370) | coding (848/1689 nt) | ilvB | acetohydroxy acid synthase I subunit IlvB | |||||
| * | ? | NC_000913 | 2704268 = | 54 (0.550) | 3 (0.030) | 3/492 | 6.0 | 3.5% | intergenic (‑205/+67) | rnc/lepB | RNase III/signal peptidase I |
| ? | NC_000913 | = 4450292 | 111 (1.130) | coding (331/957 nt) | ytfQ | galactofuranose ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 2685274 | 66 (0.670) | 3 (0.030) | 3/490 | 6.0 | 4.0% | coding (234/1254 nt) | glyA | serine hydroxymethyltransferase |
| ? | NC_000913 | 3154008 = | 78 (0.800) | coding (446/660 nt) | yghB | DedA family protein YghB | |||||
| * | ? | NC_000913 | = 1187522 | 100 (1.020) | 3 (0.030) +A |
3/490 | 6.0 | 2.7% | coding (719/1122 nt) | roxA | 50S ribosomal protein L16‑arginine 3‑hydroxylase |
| ? | NC_000913 | 4285880 = | 119 (1.220) | coding (1492/1959 nt) | acs | acetyl‑CoA synthetase (AMP‑forming) | |||||
| * | ? | NC_000913 | 1135349 = | 129 (1.320) | 3 (0.030) | 3/490 | 6.0 | 2.3% | coding (621/783 nt) | flgG | flagellar basal‑body rod protein FlgG |
| ? | NC_000913 | = 3089244 | 128 (1.310) | coding (961/1395 nt) | galP | galactose:H(+) symporter | |||||
| * | ? | NC_000913 | = 970864 | 109 (1.110) | 3 (0.030) | 3/492 | 6.0 | 2.4% | coding (13/747 nt) | kdsB | 3‑deoxy‑manno‑octulosonate cytidylyltransferase |
| ? | NC_000913 | 3047867 = | 133 (1.360) | coding (1175/2874 nt) | gcvP | glycine decarboxylase | |||||
| * | ? | NC_000913 | 556761 = | 100 (1.020) | 3 (0.030) | 3/492 | 6.0 | 3.2% | coding (113/213 nt) | ybcJ | putative RNA‑binding protein YbcJ |
| ? | NC_000913 | = 3732663 | 79 (0.810) | coding (463/1542 nt) | xylG | xylose ABC transporter ATP binding subunit | |||||
| * | ? | NC_000913 | = 228457 | NA (NA) | 3 (0.030) | 3/490 | 6.0 | 4.1% | noncoding (2699/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 1258774 = | 71 (0.730) | intergenic (‑261/‑17) | pth/ychH | peptidyl‑tRNA hydrolase/stress‑induced protein | |||||