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 40 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,606,215 | 0 | G | . | 77.8% | 238.3 / 105.9 | 90 | noncoding (72/87 nt) | leuP | tRNA‑Leu |
| * | NC_000913 | 1,001,023 | 0 | A | . | 65.3% | 126.6 / 198.3 | 101 | coding (1808/2601 nt) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 1,097,158 | 0 | C | T | 50.0% | ‑3.2 / 29.4 | 20 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,433,340 | 0 | G | T | 40.0% | 99.2 / 13.5 | 75 | S196Y (TCC→TAC) | accD | acetyl‑CoA carboxyltransferase subunit beta |
| * | NC_000913 | 1,097,118 | 0 | C | A | 38.1% | 15.0 / 16.8 | 21 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,054,894 | 0 | G | T | 36.8% | 140.9 / 50.3 | 114 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,427,992 | 0 | G | T | 36.6% | 83.6 / 14.6 | 82 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.5% | 189.2 / 37.5 | 114 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,360,965 | 0 | C | A | 32.4% | 288.3 / 20.3 | 142 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,741,871 | 0 | G | T | 30.6% | 257.4 / 28.5 | 147 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,722,838 | 0 | G | T | 30.5% | 192.1 / 10.8 | 95 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 2,477,265 | 0 | A | C | 30.3% | 193.3 / 27.3 | 99 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,335,034 | 0 | G | T | 30.2% | 206.1 / 16.1 | 116 | intergenic (+205/‑114) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 4,136,467 | 0 | A | C | 29.6% | 184.3 / 20.5 | 98 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 2,365,840 | 0 | T | G | 28.8% | 215.6 / 18.1 | 140 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 4,074,572 | 0 | C | A | 28.5% | 270.2 / 15.3 | 144 | P278P (CCC→CCA) | yihV | 6‑deoxy‑6‑sulfofructose kinase |
| * | NC_000913 | 847,955 | 0 | G | A | 27.8% | 132.5 / 35.6 | 90 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,470,627 | 0 | C | A | 27.8% | 228.2 / 12.4 | 108 | pseudogene (109/3495 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 2,855,852 | 0 | C | A | 27.7% | 159.2 / 15.2 | 83 | L505L (CTC→CTA) | fhlA | DNA‑binding transcriptional activator FhlA |
| * | NC_000913 | 2,771,139 | 0 | G | T | 26.4% | 265.0 / 11.1 | 129 | intergenic (+15/‑9) | yfjS/yfjT | inner membrane lipoprotein YfjS/uncharacterized protein YfjT |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 23 (0.230) | 22/590 | 2.2 | 13.1% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 4093211 = | 152 (1.520) | coding (228/315 nt) | rhaM | L‑rhamnose mutarotase | |||||
| * | ? | NC_000913 | = 4093215 | 163 (1.610) | 26 (0.260) | 22/598 | 2.3 | 13.8% | coding (224/315 nt) | rhaM | L‑rhamnose mutarotase |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4215329 | 145 (1.430) | 22 (0.220) | 19/582 | 2.5 | 13.5% | intergenic (+120/‑149) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A |
| ? | NC_000913 | 4215341 = | 142 (1.440) | intergenic (+132/‑137) | metA/aceB | homoserine O‑succinyltransferase/malate synthase A | |||||
| * | ? | NC_000913 | = 4404935 | 117 (1.160) | 18 (0.180) | 15/598 | 3.2 | 13.4% | coding (249/1299 nt) | purA | adenylosuccinate synthetase |
| ? | NC_000913 | 4404945 = | 116 (1.150) | coding (259/1299 nt) | purA | adenylosuccinate synthetase | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 16 (0.160) | 15/598 | 3.2 | 19.8% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2317260 | 65 (0.640) | coding (2617/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | = 2665911 | 85 (0.840) | 17 (0.170) | 14/596 | 3.3 | 16.4% | coding (477/1281 nt) | csiE | stationary phase‑inducible protein CsiE |
| ? | NC_000913 | 2665917 = | 89 (0.880) | coding (483/1281 nt) | csiE | stationary phase‑inducible protein CsiE | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 14 (0.140) | 13/598 | 3.5 | 18.7% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2317256 = | 61 (0.600) | coding (2621/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | 1651437 = | 26 (0.260) | 15 (0.150) | 13/598 | 3.5 | 36.6% | noncoding (595/706 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 11 (0.110) | 11/598 | 3.9 | 7.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3365059 | 142 (1.400) | coding (2253/2382 nt) | yhcD | putative fimbrial usher protein YhcD | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 14 (0.140) | 11/598 | 3.9 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382483 | NA (NA) | noncoding (1224/1331 nt) | IS2 | repeat region | |||||