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 145 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 | 44.0% | 60.9 / 26.7 | 77 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 3,862,664 | 0 | C | G | 39.3% | 30.4 / 26.3 | 62 | 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 | 39.2% | 77.7 / 28.9 | 112 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 3,745,001 | 0 | T | G | 38.6% | 113.3 / 19.8 | 91 | G66G (GGT→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,745,019 | 0 | C | G | 38.5% | 79.8 / 26.4 | 78 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 3,862,667 | 0 | G | A | 37.7% | 67.5 / 24.8 | 61 | 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 | 36.8% | 114.1 / 24.4 | 100 | G243G (GGT→GGG) | glyA | serine hydroxymethyltransferase |
| * | NC_000913 | 3,862,662 | 0 | T | G | 35.5% | 60.2 / 13.7 | 62 | pseudogene (942/1617 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 | 3,745,397 | 0 | A | C | 35.4% | 211.0 / 25.7 | 136 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 540,558 | 0 | T | G | 32.9% | 281.4 / 51.4 | 149 | intergenic (+50/‑7) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| * | NC_000913 | 249,538 | 0 | T | G | 30.6% | 218.3 / 14.2 | 135 | pseudogene (533/1713 nt) | lfhA | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| * | NC_000913 | 3,862,668 | 0 | A | G | 30.5% | 80.1 / 12.8 | 59 | pseudogene (936/1617 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 | 4,571,183 | 0 | A | C | 30.4% | 227.2 / 12.5 | 92 | V131G (GTG→GGG) | yjiR | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| * | NC_000913 | 4,223,597 | 0 | C | T | 29.3% | 268.3 / 42.7 | 134 | R11K (AGA→AAA) | iclR | transcriptional repressor |
| * | NC_000913 | 2,378,968 | 0 | C | T | 29.3% | 117.8 / 31.8 | 82 | E98K (GAA→AAA) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| * | NC_000913 | 354,288 | 0 | T | G | 29.1% | 295.7 / 27.7 | 110 | V528G (GTG→GGG) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 354,282 | 0 | T | G | 28.6% | 286.0 / 16.5 | 105 | V526G (GTT→GGT) | prpE | propionate‑‑CoA ligase |
| * | NC_000913 | 3,862,670 | 0 | T | A | 28.3% | 46.3 / 12.8 | 63 | pseudogene (934/1617 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 | 4,361,531 | 0 | T | G | 28.3% | 493.9 / 38.3 | 194 | H135P (CAC→CCC) | cadC | cadBA operon transcriptional activator |
| * | NC_000913 | 1,383,722 | 0 | G | A | 28.2% | 354.4 / 75.9 | 181 | F80F (TTC→TTT) | ycjW | LacI family putative transcriptional repressor |
| Marginal new junction evidence (lowest skew 10 of 83 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 264 (1.070) | 55 (0.250) | 44/302 | 3.5 | 21.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 167 (0.750) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207790 = | 255 (1.040) | 52 (0.230) | 41/302 | 3.9 | 20.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 170 (0.760) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3563404 = | 228 (0.930) | 14 (0.060) | 12/320 | 10.5 | 5.9% | coding (1392/1506 nt) | glpD | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding |
| ? | NC_000913 | 3563422 = | 225 (0.960) | coding (1410/1506 nt) | glpD | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding | |||||
| * | ? | NC_000913 | 225456 = | 68 (0.280) | 10 (0.050) +22 bp |
7/290 | 12.0 | 6.5% | noncoding (76/77 nt) | ileV | tRNA‑Ile |
| ? | NC_000913 | = 2518117 | 263 (1.070) | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala | |||||
| * | ? | NC_000913 | 624301 = | 227 (0.920) | 8 (0.030) | 8/316 | 12.1 | 3.6% | coding (210/957 nt) | fepB | ferrienterobactin ABC transporter periplasmic binding protein |
| ? | NC_000913 | 624332 = | 213 (0.920) | coding (179/957 nt) | fepB | ferrienterobactin ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 3248538 | 282 (1.150) | 9 (0.040) | 8/318 | 12.2 | 3.3% | coding (100/384 nt) | mzrA | modulator of EnvZ/OmpR regulon |
| ? | NC_000913 | = 3248548 | 267 (1.140) | coding (110/384 nt) | mzrA | modulator of EnvZ/OmpR regulon | |||||
| * | ? | NC_000913 | = 2518117 | 263 (1.070) | 10 (0.050) +22 bp |
6/290 | 12.5 | 4.2% | intergenic (‑1/+39) | alaX/alaW | tRNA‑Ala/tRNA‑Ala |
| ? | NC_000913 | = 3427077 | NA (NA) | noncoding (76/77 nt) | ileU | tRNA‑Ile | |||||
| * | ? | NC_000913 | 2077808 = | 317 (1.290) | 8 (0.040) | 7/310 | 12.5 | 2.5% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 336 (1.470) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3867985 = | 218 (0.890) | 7 (0.030) | 7/318 | 12.7 | 3.2% | coding (258/333 nt) | yidQ | DUF1375 family outer membrane protein |
| ? | NC_000913 | 3868014 = | 218 (0.930) | coding (287/333 nt) | yidQ | DUF1375 family outer membrane protein | |||||
| * | ? | NC_000913 | = 243009 | 202 (0.820) | 10 (0.040) | 7/320 | 12.7 | 4.1% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 276 (1.170) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||