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 237 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,145,167 | 0 | G | T | 40.0% | 62.1 / 21.8 | 60 | intergenic (+40/+25) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 3,199,794 | 0 | C | T | 37.7% | 184.8 / 78.7 | 146 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 2,145,170 | 0 | G | T | 35.0% | 70.4 / 11.7 | 60 | intergenic (+43/+22) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 32.5% | 153.2 / 17.9 | 81 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 32.0% | 281.5 / 39.1 | 122 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 2,230,380 | 0 | T | C | 31.9% | 214.1 / 32.2 | 115 | T285A (ACG→GCG) | mglC | galactose/methyl galactoside ABC transporter permease MglC |
| * | NZ_CP009273 | 2,221,754 | 0 | T | C | 31.8% | 109.7 / 14.5 | 69 | pseudogene (484/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 31.0% | 79.9 / 13.3 | 59 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 295,837 | 0 | A | G | 30.8% | 152.5 / 30.7 | 104 | L270P (CTC→CCC) | paoC | aldehyde oxidoreductase molybdenum‑binding subunit PaoC |
| * | NZ_CP009273 | 748,581 | 0 | T | A | 30.7% | 267.6 / 41.7 | 128 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 383,643 | 0 | T | G | 30.2% | 234.5 / 12.0 | 107 | G131G (GGT→GGG) | tauD | taurine dioxygenase |
| * | NZ_CP009273 | 3,171,107 | 0 | C | A | 30.1% | 341.2 / 72.1 | 166 | E55* (GAG→TAG) | nudF | ADP‑ribose diphosphatase |
| * | NZ_CP009273 | 2,601,603 | 0 | T | G | 30.1% | 156.5 / 10.1 | 93 | V443G (GTG→GGG) | hyfF | hydrogenase 4 subunit F |
| * | NZ_CP009273 | 1,240,690 | 0 | G | T | 29.9% | 321.8 / 48.9 | 144 | L25F (TTG→TTT) | BW25113_RS06225 | protein YcgY |
| * | NZ_CP009273 | 3,806,632 | 0 | C | T | 29.7% | 149.5 / 33.6 | 101 | S181L (TCG→TTG) | coaBC | bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC |
| * | NZ_CP009273 | 3,781,385 | 0 | T | G | 29.2% | 306.1 / 21.1 | 149 | G396G (GGT→GGG) | envC | murein hydrolase activator EnvC |
| * | NZ_CP009273 | 4,326,718 | 0 | T | A | 28.7% | 238.7 / 39.5 | 131 | Y44F (TAT→TTT) | adiC | arginine/agmatine antiporter |
| * | NZ_CP009273 | 429,090 | 0 | T | G | 28.5% | 208.9 / 21.0 | 153 | G60G (GGT→GGG) | ribD | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase RibD |
| * | NZ_CP009273 | 3,199,811 | 0 | C | A | 28.4% | 255.6 / 53.6 | 143 | intergenic (‑196/‑11) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 3,888,580 | 0 | T | A | 27.9% | 309.2 / 35.2 | 147 | intergenic (+2/+52) | yieF/adeP | class I chromate reductase YieF/adenine permease AdeP |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | = 3416707 | 111 (0.620) | 18 (0.440) +191 bp |
12/114 | 4.1 | 41.5% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416716 = | 110 (0.610) | intergenic (+163/+68) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 76 (0.420) | 108 (0.600) | 80/496 | 4.1 | 53.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 110 (0.610) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 81 (0.450) | 87 (0.500) +AATTCC |
62/484 | 6.5 | 43.5% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 151 (0.840) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 360286 | 112 (0.620) | 29 (0.160) +AATTC |
24/486 | 17.2 | 21.2% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 108 (0.600) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 108 (0.600) | 9 (0.080) +93 bp |
6/310 | 20.2 | 11.6% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 111 (0.620) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 2940826 | 92 (0.510) | 4 (0.030) | 4/330 | 23.0 | 5.7% | intergenic (+4/‑30) | BW25113_RS14635/BW25113_RS14640 | tRNA‑Met/tRNA‑Met |
| ? | NZ_CP009273 | 2941047 = | 72 (0.600) | intergenic (+5/+69) | BW25113_RS14645/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NZ_CP009273 | 360104 = | 81 (0.450) | 12 (0.070) +AATTCC |
10/484 | 24.6 | 9.3% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 160 (0.890) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 108 (0.600) | 11 (0.060) +GAATTAATTCC |
8/474 | 25.7 | 8.2% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 151 (0.840) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 4315706 = | 168 (0.930) | 4 (0.030) +50 bp |
4/396 | 26.1 | 2.6% | intergenic (‑148/+510) | yjdN/yjdM | VOC family metalloprotein YjdN/zinc ribbon domain‑containing protein YjdM |
| ? | NZ_CP009273 | = 4316155 | 201 (1.120) | intergenic (‑597/+61) | yjdN/yjdM | VOC family metalloprotein YjdN/zinc ribbon domain‑containing protein YjdM | |||||
| * | ? | NZ_CP009273 | 4532499 = | 193 (1.070) | 6 (0.030) | 6/478 | 27.5 | 3.1% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 190 (1.100) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||