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 48 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,151,686 | 0 | G | T | 50.0% | ‑6.1 / 12.9 | 24 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 417,533 | 0 | T | G | 43.2% | 33.8 / 14.3 | 46 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 3,862,664 | 0 | C | G | 36.7% | 30.1 / 18.0 | 51 | pseudogene (940/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 433,649 | 0 | T | G | 34.6% | 107.5 / 19.3 | 110 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,862,667 | 0 | G | A | 33.3% | 62.4 / 19.6 | 54 | pseudogene (937/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 2,684,779 | 0 | A | C | 32.2% | 125.4 / 18.8 | 93 | G243G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| * | NC_000913 | 753,125 | 0 | T | A | 28.6% | 140.5 / 22.6 | 63 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| * | NC_000913 | 1,265,473 | 0 | T | G | 28.6% | 352.9 / 13.1 | 134 | G154G (GGT→GGG) | prfA | peptide chain release factor RF‑1 |
| * | NC_000913 | 4,101,514 | 0 | G | T | 28.4% | 164.9 / 27.7 | 67 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase, Mn/2‑keto‑3‑deoxy‑D‑gluconate transporter |
| * | NC_000913 | 3,930,718 | 0 | T | G | 28.2% | 186.5 / 14.0 | 79 | T126P (ACC→CCC) | ravA | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| * | NC_000913 | 4,429,984 | 0 | T | G | 27.7% | 242.7 / 19.7 | 95 | L41V (TTG→GTG) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | NC_000913 | 3,782,913 | 0 | A | C | 26.9% | 91.6 / 13.7 | 78 | V250G (GTG→GGG) | gpsA | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| * | NC_000913 | 540,558 | 0 | T | G | 26.0% | 265.5 / 42.8 | 129 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 3,548,925 | 0 | A | C | 25.6% | 345.5 / 24.5 | 160 | G382G (GGT→GGG) | malQ | 4‑alpha‑glucanotransferase (amylomaltase) |
| * | NC_000913 | 1,265,482 | 0 | T | G | 24.8% | 307.2 / 22.9 | 123 | G157G (GGT→GGG) | prfA | peptide chain release factor RF‑1 |
| * | NC_000913 | 1,258,996 | 0 | T | G | 24.2% | 297.8 / 16.5 | 129 | V69G (GTG→GGG) | ychH | DUF2583 family putative inner membrane protein |
| * | NC_000913 | 825,235 | 0 | T | A | 24.2% | 231.9 / 27.1 | 122 | M292L (ATG→TTG) | ybhR | putative ABC transporter permease |
| * | NC_000913 | 766,716 | 0 | G | T | 23.9% | 143.6 / 20.4 | 67 | A245S (GCG→TCG) | mngA | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component |
| * | NC_000913 | 1,383,722 | 0 | G | A | 23.8% | 233.5 / 25.0 | 102 | F80F (TTC→TTT) | ycjW | LacI family putative transcriptional repressor |
| * | NC_000913 | 3,760,377 | 0 | G | A | 23.8% | 163.5 / 17.8 | 101 | F291F (TTC→TTT) | selA | selenocysteine synthase |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 221 (1.130) | 37 (0.210) | 30/314 | 4.0 | 16.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 180 (1.020) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 215 (1.100) | 25 (0.140) | 23/314 | 5.1 | 11.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 176 (1.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 3619291 | 68 (0.350) | 13 (0.070) | 6/324 | 10.4 | 25.1% | coding (100/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3619450 | 14 (0.080) | coding (259/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 3619291 | 69 (0.350) | 12 (0.070) | 5/324 | 10.9 | 23.8% | coding (100/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3762441 | 12 (0.070) | coding (259/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 729682 | 101 (0.520) | 10 (0.050) | 5/324 | 10.9 | 10.0% | coding (100/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 729841 | 86 (0.470) | coding (259/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | = 2817942 | 186 (0.950) | 6 (0.030) | 4/306 | 11.1 | 3.7% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 147 (0.850) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 1209618 | 210 (1.080) | 17 (0.100) | 4/316 | 11.3 | 8.2% | pseudogene (2/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| ? | NC_000913 | 2471897 = | 188 (1.060) | pseudogene (226/579 nt) | yfdL | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 729852 | 86 (0.440) | 9 (0.050) | 4/324 | 11.4 | 9.6% | coding (270/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3762271 | 89 (0.490) | coding (89/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 4614257 = | NA (NA) | 8 (0.040) | 4/326 | 11.5 | NA | noncoding (1/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913 | = 4614660 | NA (NA) | intergenic (+400/+20) | yjjV/yjjW | putative DNase/putative pyruvate formate lyase activating enzyme | |||||
| * | ? | NC_000913 | = 2361573 | 137 (0.700) | 4 (0.020) | 4/328 | 11.5 | 2.6% | coding (639/783 nt) | rhmR | putative DNA‑binding transcriptional regulator for the rhm operon |
| ? | NC_000913 | = 2361755 | 171 (0.930) | coding (457/783 nt) | rhmR | putative DNA‑binding transcriptional regulator for the rhm operon | |||||