mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 89 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 417,533 | 0 | T | G | 57.7% | ‑5.8 / 16.4 | 26 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 433,634 | 0 | T | G | 36.2% | 52.8 / 12.3 | 60 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 35.9% | 70.4 / 21.4 | 39 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| * | NC_000913 | 433,649 | 0 | T | G | 35.1% | 36.1 / 10.5 | 57 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,531,463 | 0 | A | C | 31.9% | 245.3 / 22.2 | 119 | V326G (GTG→GGG) | yhgE | DUF4153 family putative inner membrane protein |
| * | NC_000913 | 2,332,823 | 0 | A | G | 31.7% | 74.4 / 12.9 | 42 | pseudogene (1580/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| * | NC_000913 | 2,745,089 | 0 | A | C | 30.6% | 131.9 / 13.2 | 62 | V84G (GTG→GGG) | trmD | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| * | NC_000913 | 1,445,981 | 0 | T | G | 30.4% | 202.5 / 10.9 | 93 | G34G (GGT→GGG) | ydbL | DUF1318 family protein |
| * | NC_000913 | 4,442,162 | 0 | A | T | 30.2% | 211.3 / 38.8 | 97 | D5E (GAT→GAA) | msrA | methionine sulfoxide reductase A |
| * | NC_000913 | 3,520,751 | 0 | G | T | 29.1% | 211.1 / 34.0 | 110 | T90K (ACA→AAA) | hofP | DNA catabolic protein |
| * | NC_000913 | 1,383,722 | 0 | G | A | 28.8% | 123.0 / 34.9 | 74 | F80F (TTC→TTT) | ycjW | LacI family putative transcriptional repressor |
| * | NC_000913 | 75,079 | 0 | C | T | 28.6% | 24.5 / 12.5 | 21 | L134L (CTG→CTA) | thiB | thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,149,907 | 0 | A | C | 28.6% | 139.0 / 12.0 | 91 | V360G (GTG→GGG) | yegI | protein kinase‑related putative non‑specific DNA‑binding protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.4% | 233.0 / 119.2 | 149 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 3,895,556 | 0 | T | C | 28.4% | 142.3 / 11.5 | 67 | M352V (ATG→GTG) | adeP | adenine permease, high affinity; adenine:H+ symporter |
| * | NC_000913 | 691,847 | 0 | A | G | 28.1% | 291.0 / 22.1 | 131 | intergenic (‑63/+27) | ybeX/ybeY | putative ion transport/ssRNA‑specific endoribonuclease; 16S rRNA 3' end maturation and quality control co‑endoribonuclease working with RNase R; rRNA transcription antitermination factor |
| * | NC_000913 | 3,665,702 | 0 | C | A | 27.7% | 196.5 / 31.0 | 83 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 647,210 | 0 | A | C | 27.6% | 150.1 / 14.9 | 76 | G100G (GGT→GGG) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| * | NC_000913 | 3,757,668 | 0 | C | T | 26.7% | 122.6 / 13.9 | 60 | A54T (GCA→ACA) | yiaY | L‑threonine dehydrogenase |
| * | NC_000913 | 3,813,272 | 0 | C | T | 26.5% | 79.4 / 22.3 | 49 | S181L (TCG→TTG) | dfp | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| 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 | 1207790 = | 165 (1.200) | 29 (0.230) | 27/304 | 2.2 | 18.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 109 (0.870) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 165 (1.200) | 22 (0.180) | 21/304 | 2.9 | 14.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 109 (0.870) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1373284 | 174 (1.260) | 5 (0.040) | 5/320 | 6.5 | 3.1% | coding (63/882 nt) | ycjO | putative sugar ABC transporter permease |
| ? | NC_000913 | = 1373292 | 148 (1.130) | coding (71/882 nt) | ycjO | putative sugar ABC transporter permease | |||||
| * | ? | NC_000913 | = 2213711 | 120 (0.870) | 3 (0.020) | 3/332 | 7.6 | 2.6% | coding (934/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT |
| ? | NC_000913 | 2213753 = | 103 (0.760) | coding (892/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT | |||||