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 140 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 73.0% | 46.8 / 20.1 | 37 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 72.2% | 42.7 / 17.3 | 37 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 578,605 | 0 | T | G | 58.3% | 185.4 / inf | 255 | K97Q (AAA→CAA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,729 | 0 | A | G | 57.7% | 164.1 / inf | 273 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,571 | 0 | C | T | 56.5% | 112.2 / inf | 246 | intergenic (+3/+29) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 578,574 | 0 | A | C | 56.5% | 155.6 / 297.8 | 248 | intergenic (+6/+26) | rzpD/borD | putative prophage endopeptidase RzpD/prophage lipoprotein BorD |
| * | NC_000913 | 566,651 | 0 | T | C | 55.7% | 100.7 / 273.2 | 203 | intergenic (‑673/‑33) | intD/renD | putative integrase/protein RenD |
| * | NC_000913 | 579,457 | 0 | A | G | 55.3% | 151.8 / inf | 365 | I46I (ATT→ATC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,385 | 0 | A | G | 54.6% | 121.6 / inf | 345 | N70N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,271 | 0 | G | A | 54.1% | 78.7 / inf | 308 | H108H (CAC→CAT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,285 | 0 | T | C | 54.0% | 66.0 / inf | 314 | I104V (ATT→GTT) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,502 | 0 | A | G | 53.4% | 101.9 / inf | 411 | N31N (AAT→AAC) | ybcV | DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 580,115 | 0 | C | T | 53.1% | 56.8 / inf | 229 | intergenic (+29/+136) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| * | NC_000913 | 578,809 | 0 | T | C | 52.9% | 63.8 / inf | 274 | T29A (ACA→GCA) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 579,127 | 0 | T | C | 52.8% | 55.5 / inf | 264 | intergenic (‑234/+57) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 566,597 | 0 | T | C | 52.5% | 30.2 / 269.3 | 179 | intergenic (‑619/‑87) | intD/renD | putative integrase/protein RenD |
| * | NC_000913 | 579,134 | 0 | T | C | 52.5% | 65.6 / inf | 261 | intergenic (‑241/+50) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 579,004 | 0 | C | T | 52.4% | 17.9 / inf | 290 | intergenic (‑111/+180) | borD/ybcV | prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV |
| * | NC_000913 | 578,811 | 0 | T | G | 52.2% | 84.4 / inf | 274 | Q28P (CAG→CCG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 580,119 | 0 | A | G | 52.0% | 29.5 / inf | 226 | intergenic (+33/+132) | ybcW/ylcI | uncharacterized protein YbcW/DUF3950 domain‑containing protein YlcI |
| 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 | = 696741 | 77 (0.720) | 10 (0.130) | 10/442 | 5.3 | 14.9% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 57 (0.720) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 781222 | 57 (0.530) | 9 (0.110) | 7/446 | 6.5 | 14.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 61 (0.760) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 781222 | 57 (0.530) | 8 (0.100) | 6/446 | 7.0 | 14.0% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 56 (0.700) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 1286906 | 62 (0.580) | 9 (0.090) | 7/558 | 7.8 | 13.2% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 61 (0.610) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4392437 | 95 (0.890) | 5 (0.060) | 4/442 | 8.0 | 6.4% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 76 (0.960) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 1287262 | 51 (0.480) | 7 (0.070) | 5/556 | 8.8 | 12.6% | noncoding (67/85 nt) | tyrV | tRNA‑Tyr |
| ? | NC_000913 | 1287382 = | 50 (0.500) | intergenic (‑54/+156) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2357690 | 100 (0.930) | 5 (0.050) | 4/548 | 9.3 | 5.2% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 89 (0.910) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1287084 | 59 (0.550) | 4 (0.040) | 4/558 | 9.4 | 6.4% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 61 (0.610) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 696505 | 89 (0.830) | 3 (0.030) | 3/538 | 9.8 | 3.9% | intergenic (‑1/+37) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 696832 = | 68 (0.710) | intergenic (‑2/+33) | glnW/glnU | tRNA‑Gln/tRNA‑Gln | |||||
| * | ? | NC_000913 | 2817783 = | 117 (1.090) | 3 (0.030) | 3/558 | 10.0 | 3.1% | intergenic (‑280/+1) | yqaB/argQ | fructose‑1‑phosphate phosphatase YqaB/tRNA‑Arg |
| ? | NC_000913 | = 2817922 | 76 (0.760) | intergenic (‑62/+137) | argQ/argZ | tRNA‑Arg/tRNA‑Arg | |||||