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 108 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 | 51.5% | ‑5.0 / 22.3 | 33 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 2,151,689 | 0 | G | T | 51.5% | ‑5.0 / 15.1 | 33 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 417,533 | 0 | T | G | 47.3% | 39.0 / 17.8 | 56 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 3,862,661 | 0 | T | G | 35.9% | 34.4 / 10.7 | 42 | pseudogene (943/1617 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 | 34.2% | 110.5 / 27.7 | 115 | G65G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 753,125 | 0 | T | A | 32.5% | 171.6 / 43.7 | 83 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial‑like adhesin protein/citrate synthase |
| * | NC_000913 | 3,862,677 | 0 | G | A | 31.2% | 8.9 / 12.2 | 39 | pseudogene (927/1617 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 | 4,429,984 | 0 | T | G | 30.8% | 242.3 / 23.0 | 107 | L41V (TTG→GTG) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | NC_000913 | 433,634 | 0 | T | G | 30.2% | 148.8 / 20.5 | 123 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 4,429,990 | 0 | A | T | 29.7% | 243.2 / 42.0 | 113 | M43L (ATG→TTG) | cycA | D‑alanine/D‑serine/glycine transporter |
| * | NC_000913 | 3,844,219 | 0 | T | G | 29.5% | 286.4 / 11.4 | 122 | F86V (TTT→GTT) | adeD | cryptic adenine deaminase |
| * | NC_000913 | 2,608,244 | 0 | T | G | 29.3% | 161.6 / 14.3 | 99 | V443G (GTG→GGG) | hyfF | hydrogenase 4, membrane subunit |
| * | NC_000913 | 3,745,019 | 0 | C | G | 29.0% | 85.1 / 17.7 | 69 | G72G (GGC→GGG) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 2,151,676 | 0 | C | G | 28.2% | 98.6 / 14.0 | 39 | intergenic (+30/+35) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 599,579 | 0 | T | G | 27.8% | 257.7 / 19.4 | 108 | V289G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 1,876,015 | 0 | A | G | 27.7% | 259.5 / 29.4 | 114 | I115V (ATT→GTT) | yeaN | putative MFS transporter, inner membrane protein |
| * | NC_000913 | 1,658,167 | 0 | G | T | 27.5% | 154.8 / 16.7 | 70 | L33F (TTG→TTT) | ynfE | putative selenate reductase, periplasmic |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.5% | 334.5 / 191.0 | 218 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 4,098,391 | 0 | A | C | 27.3% | 260.6 / 25.7 | 131 | Y219S (TAC→TCC) | rhaS | transcriptional activator of rhaBAD and rhaT |
| * | NC_000913 | 2,151,710 | 0 | C | A | 27.3% | 97.7 / 12.6 | 44 | intergenic (+64/+1) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| 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 = | 241 (1.190) | 36 (0.190) | 31/324 | 4.3 | 14.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 194 (1.050) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 227 (1.120) | 39 (0.210) | 27/324 | 4.9 | 16.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 189 (1.020) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2765420 = | 271 (1.330) | 8 (0.050) | 7/268 | 9.2 | 4.2% | intergenic (‑267/+93) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| ? | NC_000913 | = 2765411 | 158 (1.040) | intergenic (‑258/+102) | yfjL/yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 4289016 = | 228 (1.120) | 8 (0.040) | 8/338 | 10.2 | 3.6% | coding (1253/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome |
| ? | NC_000913 | 4289092 = | 208 (1.080) | coding (1329/1437 nt) | nrfA | nitrite reductase, formate‑dependent, cytochrome | |||||
| * | ? | NC_000913 | = 2331858 | 209 (1.030) | 7 (0.040) | 7/340 | 10.7 | 3.4% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| ? | NC_000913 | = 2331859 | 196 (1.010) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein | |||||
| * | ? | NC_000913 | = 4542690 | 69 (0.340) | 5 (0.030) | 5/338 | 11.6 | 4.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 129 (0.670) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | 1082864 = | 227 (1.120) | 5 (0.030) | 5/336 | 11.6 | 2.5% | coding (622/1128 nt) | efeO | inactive ferrous ion transporter EfeUOB |
| ? | NC_000913 | 1083032 = | 183 (0.960) | coding (790/1128 nt) | efeO | inactive ferrous ion transporter EfeUOB | |||||
| * | ? | NC_000913 | = 3010000 | 198 (0.980) | 6 (0.030) | 5/340 | 11.7 | 3.1% | intergenic (+25/‑28) | ygeY/hyuA | putative peptidase/D‑stereospecific phenylhydantoinase |
| ? | NC_000913 | = 3010004 | 182 (0.940) | intergenic (+29/‑24) | ygeY/hyuA | putative peptidase/D‑stereospecific phenylhydantoinase | |||||
| * | ? | NC_000913 | = 1946034 | 186 (0.920) | 6 (0.030) | 5/340 | 11.7 | 3.3% | intergenic (‑58/+81) | ruvA/yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized protein |
| ? | NC_000913 | = 1946036 | 178 (0.920) | intergenic (‑60/+79) | ruvA/yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized protein | |||||
| * | ? | NC_000913 | 3515982 = | 209 (1.030) | 5 (0.030) | 4/338 | 12.2 | 2.4% | intergenic (‑69/+38) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| ? | NC_000913 | 3516010 = | 201 (1.040) | intergenic (‑97/+10) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring | |||||