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 162 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 | 41.4% | 37.4 / 65.2 | 58 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 729,710 | 0 | T | G | 35.7% | 150.6 / 20.5 | 98 | V43G (GTG→GGG) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 1,826,379 | 0 | T | C | 35.1% | 126.5 / 22.0 | 78 | E182G (GAG→GGG) | astE | succinylglutamate desuccinylase |
| * | NC_000913 | 786,855 | 0 | A | C | 34.1% | 283.7 / 21.0 | 140 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 1,679,304 | 0 | A | C | 33.0% | 191.5 / 19.0 | 104 | Y293S (TAC→TCC) | ydgH | DUF1471 domain‑containing protein YdgH |
| * | NC_000913 | 1,621,118 | 0 | A | C | 31.8% | 190.0 / 13.1 | 109 | V7G (GTG→GGG) | eamA | cysteine/O‑acetylserine exporter EamA |
| * | NC_000913 | 2,483,254 | 0 | G | A | 31.0% | 105.6 / 20.8 | 58 | S29L (TCA→TTA) | emrK | tripartite efflux pump membrane fusion protein EmrK |
| * | NC_000913 | 989,943 | 0 | T | G | 30.6% | 188.1 / 12.9 | 126 | S138S (TCA→TCC) | pncB | nicotinate phosphoribosyltransferase |
| * | NC_000913 | 2,228,222 | 0 | T | G | 30.3% | 167.5 / 10.4 | 89 | intergenic (‑952/‑760) | yohF/yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| * | NC_000913 | 3,177,748 | 0 | C | A | 30.3% | 108.8 / 23.0 | 76 | E55* (GAG→TAG) | nudF | ADP‑sugar pyrophosphatase |
| * | NC_000913 | 4,571,183 | 0 | A | C | 30.1% | 210.5 / 13.1 | 114 | V131G (GTG→GGG) | yjiR | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| * | NC_000913 | 1,825,056 | 0 | G | A | 29.8% | 110.8 / 20.9 | 57 | intergenic (‑119/+84) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 29,486 | 0 | C | A | 29.8% | 101.2 / 18.8 | 47 | intergenic (+291/‑165) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl‑phosphate synthetase small subunit |
| * | NC_000913 | 29,496 | 0 | T | A | 29.8% | 98.8 / 13.4 | 47 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl‑phosphate synthetase small subunit |
| * | NC_000913 | 1,684,736 | 0 | A | C | 29.6% | 194.1 / 16.2 | 100 | T160P (ACC→CCC) | tus | DNA replication terminus site‑binding protein |
| * | NC_000913 | 4,027,233 | 0 | T | A | 29.6% | 187.5 / 29.5 | 98 | intergenic (+5/+376) | fre/fadA | NAD(P)H‑flavin reductase/3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 3,844,219 | 0 | T | G | 29.4% | 198.8 / 11.6 | 103 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 2,833,567 | 0 | T | G | 29.4% | 289.1 / 24.4 | 143 | G364G (GGT→GGG) | norV | anaerobic nitric oxide reductase flavorubredoxin |
| * | NC_000913 | 433,649 | 0 | T | G | 29.0% | 174.2 / 21.9 | 151 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| * | NC_000913 | 4,287,719 | 0 | T | A | 28.9% | 158.7 / 28.1 | 76 | intergenic (+52/‑45) | ytcB/nrfA | protein YtcB/cytochrome c552 nitrite reductase |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 110 (0.790) | 3 (0.030) | 3/336 | 8.6 | 3.7% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 81 (0.850) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 780629 | 131 (0.940) | 3 (0.030) | 3/340 | 8.7 | 3.3% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 85 (0.880) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 2542213 | 163 (1.170) | 4 (0.030) | 4/492 | 9.9 | 2.4% | coding (300/834 nt) | cysU | sulfate/thiosulfate ABC transporter inner membrane subunit CysU |
| ? | NC_000913 | = 2730341 | NA (NA) | noncoding (817/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3604001 | 99 (0.710) | 3 (0.020) | 3/464 | 10.2 | 2.6% | coding (243/1494 nt) | ftsY | signal recognition particle receptor |
| ? | NC_000913 | 4291401 = | 135 (1.020) | coding (926/957 nt) | nrfD | putative menaquinol‑cytochrome c reductase subunit NrfD | |||||
| * | ? | NC_000913 | = 3154820 | 118 (0.840) | 3 (0.020) +G |
3/490 | 10.4 | 2.1% | coding (399/957 nt) | yqhC | DNA‑binding transcriptional activator YqhC |
| ? | NC_000913 | = 4618676 | 158 (1.130) | coding (448/1323 nt) | deoA | thymidine phosphorylase | |||||
| * | ? | NC_000913 | = 2085979 | 168 (1.200) | 3 (0.020) | 3/492 | 10.4 | 1.8% | coding (1084/1359 nt) | plaP | putrescine:H(+) symporter PlaP |
| ? | NC_000913 | 2720195 = | 164 (1.170) | coding (243/2661 nt) | patZ | peptidyl‑lysine N‑acetyltransferase | |||||
| * | ? | NC_000913 | = 1852683 | 118 (0.840) | 3 (0.020) | 3/492 | 10.4 | 2.5% | coding (1297/1359 nt) | ydjE | putative transporter YdjE |
| ? | NC_000913 | = 3342875 | 115 (0.820) | coding (40/576 nt) | lptC | lipopolysaccharide transport system protein LptC | |||||
| * | ? | NC_000913 | = 984983 | 173 (1.240) | 3 (0.020) | 3/490 | 10.4 | 1.8% | coding (727/1191 nt) | aspC | aspartate aminotransferase |
| ? | NC_000913 | 4566535 = | 153 (1.100) | coding (712/1281 nt) | yjiN | DUF445 domain‑containing protein YjiN | |||||
| * | ? | NC_000913 | 956477 = | 112 (0.800) | 3 (0.020) +G |
3/490 | 10.4 | 2.6% | coding (156/1761 nt) | ycaO | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| ? | NC_000913 | = 3789177 | 116 (0.830) | coding (905/1035 nt) | waaH | UDP‑glucuronate:LPS(HepIII) glycosyltransferase | |||||
| * | ? | NC_000913 | 707186 = | 120 (0.860) | 3 (0.020) | 3/492 | 10.4 | 1.8% | coding (1094/1665 nt) | glnS | glutamine‑‑tRNA ligase |
| ? | NC_000913 | 4290802 = | 202 (1.450) | coding (327/957 nt) | nrfD | putative menaquinol‑cytochrome c reductase subunit NrfD | |||||