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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,427,992 | 0 | G | T | 38.2% | 104.8 / 14.6 | 89 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 3,054,888 | 0 | A | C | 35.4% | 157.6 / 10.1 | 98 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,136,467 | 0 | A | C | 34.9% | 53.2 / 13.0 | 44 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 2,767,445 | 0 | C | A | 34.8% | 213.3 / 20.3 | 113 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,756,353 | 0 | C | A | 34.4% | 157.5 / 16.4 | 96 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 3,054,886 | 0 | G | T | 34.0% | 149.4 / 29.8 | 98 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,894 | 0 | G | T | 33.7% | 131.4 / 29.8 | 98 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,288,418 | 0 | G | T | 33.1% | 238.9 / 20.2 | 133 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 2,477,265 | 0 | A | C | 33.0% | 169.4 / 29.2 | 97 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,767,443 | 0 | C | A | 32.4% | 219.6 / 15.1 | 113 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,444 | 0 | C | A | 32.4% | 218.7 / 15.0 | 113 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,543,220 | 0 | A | C | 32.0% | 169.4 / 14.9 | 100 | L18F (TTA→TTC) | rpnA | recombination‑promoting nuclease RpnA |
| * | NC_000913 | 4,296,268 | 0 | T | C | 31.8% | 49.8 / 35.7 | 45 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 847,955 | 0 | G | A | 31.4% | 128.9 / 47.3 | 105 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 866,319 | 0 | C | A | 29.2% | 200.4 / 12.2 | 113 | E16* (GAG→TAG) | moeA | molybdopterin molybdotransferase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 28.2% | 296.3 / 25.4 | 142 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 1,334,966 | 0 | A | C | 27.9% | 219.4 / 29.1 | 129 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,767,447 | 0 | C | A | 27.6% | 255.1 / 11.5 | 117 | intergenic (+92/‑263) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,335,034 | 0 | G | T | 27.2% | 243.3 / 13.8 | 136 | intergenic (+205/‑114) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,767,449 | 0 | C | A | 27.1% | 254.5 / 17.7 | 118 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 105 (1.100) | 12 (0.130) | 11/580 | 5.8 | 10.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 108 (1.170) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 123 (1.290) | 11 (0.120) | 10/580 | 6.1 | 8.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 108 (1.170) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1287329 | 74 (0.780) | 8 (0.120) | 6/424 | 6.1 | 14.0% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 46 (0.680) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 2357730 | 110 (1.160) | 8 (0.100) | 8/518 | 6.3 | 7.8% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 93 (1.130) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4606166 | 79 (0.830) | 5 (0.070) | 5/420 | 6.5 | 7.7% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 65 (0.970) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3648146 | 104 (1.090) | 6 (0.080) | 6/482 | 6.7 | 6.7% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 82 (1.070) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781222 | 51 (0.540) | 5 (0.070) | 5/446 | 6.8 | 10.5% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 47 (0.660) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 1286906 | 48 (0.500) | 8 (0.090) | 7/558 | 7.1 | 13.0% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 62 (0.700) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2653502 | 112 (1.180) | 6 (0.070) | 6/530 | 7.3 | 6.2% | intergenic (‑47/‑353) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653825 = | 81 (0.960) | intergenic (‑370/‑30) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 696441 | 71 (0.750) | 6 (0.070) | 6/574 | 7.7 | 9.3% | noncoding (64/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696877 = | 49 (0.540) | noncoding (63/75 nt) | glnU | tRNA‑Gln | |||||