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 47 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.7% | 194.5 / 46.6 | 121 | L122* (TTA→TGA) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,288,418 | 0 | G | T | 33.6% | 172.4 / 24.3 | 107 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 1,375,723 | 0 | C | A | 33.6% | 165.3 / 13.1 | 113 | S254Y (TCC→TAC) | ycjQ | D‑guloside 3‑dehydrogenase |
| * | NC_000913 | 2,767,445 | 0 | C | A | 32.4% | 204.0 / 17.0 | 109 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.7% | 214.1 / 29.7 | 142 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,136,467 | 0 | A | C | 31.5% | 80.9 / 18.5 | 54 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 1,087,628 | 0 | A | C | 31.2% | 212.5 / 11.1 | 110 | D73E (GAT→GAG) | pgaC | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| * | NC_000913 | 3,054,894 | 0 | G | T | 30.8% | 157.9 / 36.5 | 107 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 29.1% | 160.4 / 11.8 | 103 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,087,577 | 0 | A | C | 28.2% | 174.3 / 16.4 | 110 | V90V (GTT→GTG) | pgaC | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| * | NC_000913 | 1,334,966 | 0 | A | C | 27.9% | 262.4 / 16.4 | 158 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 141,849 | 0 | C | A | 27.7% | 226.0 / 11.6 | 119 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 847,955 | 0 | G | A | 27.2% | 213.7 / 51.6 | 147 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,171,557 | 0 | C | A | 27.1% | 156.5 / 60.9 | 96 | intergenic (+13/‑80) | rrlB/rrfB | 23S ribosomal RNA/5S ribosomal RNA |
| * | NC_000913 | 1,922,815 | 0 | C | A | 26.7% | 213.4 / 12.5 | 131 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,477,258 | 0 | G | A | 26.6% | 250.6 / 20.3 | 124 | D124D (GAC→GAT) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,903,015 | 0 | C | A | 26.6% | 122.7 / 23.9 | 64 | G229G (GGG→GGT) | bglB | 6‑phospho‑beta‑glucosidase B |
| * | NC_000913 | 3,269,943 | 0 | G | T | 26.3% | 120.0 / 11.8 | 81 | intergenic (+341/+273) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 147,802 | 0 | C | A | 26.3% | 209.0 / 10.7 | 118 | R279R (CGG→AGG) | rpnC | recombination‑promoting nuclease RpnC |
| * | NC_000913 | 2,477,264 | 0 | T | C | 26.1% | 248.6 / 13.3 | 120 | L122L (TTA→TTG) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| 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 | = 3648146 | 112 (1.020) | 9 (0.100) | 9/482 | 6.8 | 9.4% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 83 (0.930) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 1287084 | 66 (0.600) | 9 (0.090) | 8/558 | 8.2 | 12.9% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 60 (0.580) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1286906 | 72 (0.650) | 10 (0.100) | 8/558 | 8.2 | 13.6% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 60 (0.580) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1287262 | 83 (0.750) | 7 (0.070) | 7/556 | 8.6 | 8.7% | noncoding (67/85 nt) | tyrV | tRNA‑Tyr |
| ? | NC_000913 | 1287382 = | 69 (0.670) | intergenic (‑54/+156) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | 1096961 = | 96 (0.870) | 4 (0.050) | 4/438 | 8.7 | 5.7% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 61 (0.760) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 2357664 | 124 (1.130) | 7 (0.070) | 7/576 | 8.8 | 6.0% | coding (761/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357848 = | 100 (0.940) | intergenic (+45/+194) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4392437 | 82 (0.740) | 3 (0.040) | 3/442 | 9.4 | 4.2% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 77 (0.950) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 696830 | 68 (0.620) | 3 (0.040) | 3/444 | 9.5 | 5.6% | noncoding (1/75 nt) | glnW | tRNA‑Gln |
| ? | NC_000913 | 696940 = | 50 (0.610) | intergenic (‑1/+23) | glnU/leuW | tRNA‑Gln/tRNA‑Leu | |||||
| * | ? | NC_000913 | = 781322 | 74 (0.670) | 6 (0.060) | 4/520 | 9.8 | 8.3% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 68 (0.710) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4094350 | 76 (0.690) | 3 (0.030) | 3/516 | 10.5 | 4.5% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 63 (0.660) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||