mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,916,104 | 0 | G | T | 48.1% | 43.5 / 194.1 | 135 | D350Y (GAC→TAC) | barA | sensor histidine kinase BarA |
| * | NC_000913 | 4,226,614 | 0 | C | A | 37.7% | 109.8 / 16.5 | 77 | L929L (CTC→CTA) | metH | cobalamin‑dependent methionine synthase |
| * | NC_000913 | 12,152 | 0 | G | T | 36.0% | 119.3 / 13.3 | 86 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 2,767,445 | 0 | C | A | 34.8% | 170.0 / 17.6 | 89 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,416,088 | 0 | C | A | 34.6% | 77.2 / 11.4 | 52 | Q448K (CAG→AAG) | pta | phosphate acetyltransferase |
| * | NC_000913 | 3,054,886 | 0 | G | T | 33.6% | 200.7 / 49.7 | 122 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.4% | 353.8 / 20.2 | 191 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,477,265 | 0 | A | C | 30.6% | 164.0 / 19.2 | 85 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,408,235 | 0 | G | T | 29.7% | 101.3 / 61.6 | 74 | P225P (CCG→CCT) | alaA | glutamate‑‑pyruvate aminotransferase AlaA |
| * | NC_000913 | 2,856,087 | 0 | G | T | 28.6% | 171.7 / 11.1 | 91 | E584* (GAG→TAG) | fhlA | DNA‑binding transcriptional activator FhlA |
| * | NC_000913 | 1,334,966 | 0 | A | C | 28.0% | 156.8 / 29.5 | 107 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,543,220 | 0 | A | C | 27.8% | 258.6 / 13.3 | 145 | L18F (TTA→TTC) | rpnA | recombination‑promoting nuclease RpnA |
| * | NC_000913 | 3,226,224 | 0 | G | T | 27.5% | 345.5 / 10.1 | 167 | intergenic (+53/‑10) | ebgC/ygjI | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta/putative transporter YgjI |
| * | NC_000913 | 4,360,965 | 0 | C | A | 27.0% | 360.6 / 14.0 | 160 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 26.3% | 214.5 / 24.0 | 120 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,812,509 | 0 | G | T | 25.9% | 176.6 / 14.9 | 85 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 4,427,822 | 0 | C | A | 25.6% | 272.0 / 12.1 | 137 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 3,741,871 | 0 | G | T | 25.0% | 395.0 / 27.2 | 182 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,136,467 | 0 | A | C | 25.0% | 201.6 / 20.4 | 103 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 3,618,627 | 0 | G | T | 24.8% | 261.3 / 11.5 | 141 | E14* (GAG→TAG) | nikR | DNA‑binding transcriptional repressor NikR |
| 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 | = 3648146 | 203 (2.190) | 10 (0.130) | 10/482 | 3.6 | 5.9% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 153 (2.050) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4542690 | 145 (1.570) | 11 (0.120) | 11/580 | 4.0 | 8.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 111 (1.240) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 131 (1.410) | 12 (0.130) | 11/580 | 4.0 | 9.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 112 (1.250) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4153411 | 121 (1.310) | 7 (0.090) | 6/516 | 5.0 | 6.1% | intergenic (‑313/+285) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| ? | NC_000913 | 4153658 = | 110 (1.380) | intergenic (‑560/+38) | ppc/argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase | |||||
| * | ? | NC_000913 | = 2357736 | 75 (0.810) | 5 (0.050) +G |
5/596 | 5.9 | 6.2% | coding (833/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357933 = | 78 (0.840) | intergenic (+130/+109) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||