mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 295 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 353,601 | 0 | C | A | 41.7% | 12.7 / 13.8 | 37 | L267F (TTG→TTT) | cynR | transcriptional regulator CynR |
| * | NZ_CP009273 | 2,354,816 | 0 | A | C | 34.7% | 131.9 / 10.6 | 78 | G26G (GGT→GGG) | rhmD | L‑rhamnonate dehydratase |
| * | NZ_CP009273 | 2,145,167 | 0 | G | T | 34.5% | 98.1 / 23.3 | 87 | intergenic (+40/+25) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 34.1% | 115.5 / 27.4 | 88 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 3,837,579 | 0 | T | G | 32.4% | 479.7 / 34.7 | 219 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NZ_CP009273 | 3,856,021 | 0 | T | G | 32.3% | 106.5 / 24.5 | 97 | pseudogene (943/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 32.0% | 182.4 / 19.9 | 97 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 3,738,757 | 0 | A | C | 31.8% | 159.8 / 23.1 | 130 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate transporter large permease YiaN |
| * | NZ_CP009273 | 4,245,989 | 0 | C | T | 31.1% | 207.9 / 31.5 | 123 | E136K (GAA→AAA) | plsB | glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB |
| * | NZ_CP009273 | 2,871,023 | 0 | A | G | 30.8% | 423.6 / 49.2 | 226 | intergenic (+46/+905) | iap/cas2e | alkaline phosphatase isozyme conversion aminopeptidase/type I‑E CRISPR‑associated endoribonuclease Cas2e |
| * | NZ_CP009273 | 4,594,167 | 0 | C | T | 30.4% | 344.2 / 70.3 | 184 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 30.1% | 328.2 / 52.9 | 167 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 3,856,024 | 0 | C | G | 30.1% | 113.8 / 25.3 | 95 | pseudogene (940/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 739,585 | 0 | T | G | 29.5% | 298.6 / 11.6 | 134 | G179G (GGT→GGG) | pxpB | 5‑oxoprolinase subunit PxpB |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 29.5% | 346.3 / 67.3 | 184 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 2,601,603 | 0 | T | G | 29.5% | 236.2 / 12.2 | 139 | V443G (GTG→GGG) | hyfF | hydrogenase 4 subunit F |
| * | NZ_CP009273 | 2,145,134 | 0 | G | T | 29.4% | 227.9 / 16.8 | 87 | intergenic (+7/+58) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 883,470 | 0 | T | G | 29.2% | 490.7 / 35.9 | 211 | intergenic (+55/+120) | rcdA/ybjL | DNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter |
| * | NZ_CP009273 | 3,199,805 | 0 | C | A | 28.8% | 279.8 / 44.0 | 172 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 1,615,375 | 0 | A | C | 28.8% | 473.9 / 32.1 | 207 | V7G (GTG→GGG) | eamA | O‑acetylserine/cysteine exporter |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | = 3416707 | 147 (0.620) | 23 (0.420) +191 bp |
15/114 | 5.1 | 40.3% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416716 = | 150 (0.630) | intergenic (+163/+68) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 113 (0.480) | 112 (0.470) | 89/496 | 6.4 | 48.3% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 127 (0.540) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 120 (0.510) | 92 (0.400) +AATTCC |
71/484 | 9.1 | 36.8% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 204 (0.860) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 2940826 | 101 (0.430) | 9 (0.060) | 8/330 | 25.8 | 11.1% | intergenic (+4/‑30) | BW25113_RS14635/BW25113_RS14640 | tRNA‑Met/tRNA‑Met |
| ? | NZ_CP009273 | 2941047 = | 77 (0.490) | intergenic (+5/+69) | BW25113_RS14645/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NZ_CP009273 | = 360286 | 132 (0.560) | 22 (0.090) +AATTC |
20/486 | 25.8 | 13.8% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 149 (0.630) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 283 (1.200) | 17 (0.070) | 17/478 | 27.1 | 6.0% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 261 (1.140) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 286 (1.210) | 16 (0.070) | 16/478 | 27.7 | 5.6% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 259 (1.140) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 149 (0.630) | 4 (0.030) +93 bp |
4/310 | 28.4 | 4.1% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 147 (0.620) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 120 (0.510) | 14 (0.060) +AATTCC |
12/484 | 30.6 | 7.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 225 (0.950) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 4315706 = | 214 (0.900) | 4 (0.020) +50 bp |
3/396 | 34.4 | 2.2% | intergenic (‑148/+510) | yjdN/yjdM | VOC family metalloprotein YjdN/zinc ribbon domain‑containing protein YjdM |
| ? | NZ_CP009273 | = 4316155 | 233 (0.980) | intergenic (‑597/+61) | yjdN/yjdM | VOC family metalloprotein YjdN/zinc ribbon domain‑containing protein YjdM | |||||