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 218 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 50.0% | 31.6 / 17.2 | 38 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 5,159 | 0 | G | A | 40.4% | 75.3 / 31.0 | 57 | intergenic (+139/‑75) | thrC/yaaX | threonine synthase/DUF2502 domain‑containing protein |
| * | NZ_CP009273 | 3,199,805 | 0 | C | A | 40.0% | 82.4 / 20.5 | 71 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 748,581 | 0 | T | A | 38.9% | 111.1 / 32.4 | 72 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 4,612,067 | 0 | A | G | 38.7% | 92.3 / 25.2 | 62 | E161G (GAG→GGG) | yjjJ | type II toxin‑antitoxin system HipA family toxin YjjJ |
| * | NZ_CP009273 | 4,612,072 | 0 | A | G | 37.7% | 105.6 / 15.7 | 61 | N163D (AAT→GAT) | yjjJ | type II toxin‑antitoxin system HipA family toxin YjjJ |
| * | NZ_CP009273 | 2,476,733 | 0 | G | A | 36.4% | 153.9 / 31.6 | 88 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NZ_CP009273 | 3,941,210 | 0 | C | T | 36.2% | 111.6 / 30.2 | 69 | E40K (GAA→AAA) | hdfR | HTH‑type transcriptional regulator HdfR |
| * | NZ_CP009273 | 4,570,451 | 0 | C | T | 36.0% | 145.1 / 26.1 | 75 | E277K (GAA→AAA) | hsdS | type I restriction‑modification system specificity subunit |
| * | NZ_CP009273 | 1,322,722 | 0 | T | G | 35.7% | 151.2 / 10.2 | 70 | T216T (ACA→ACC) | yciK | YciK family oxidoreductase |
| * | NZ_CP009273 | 2,897,051 | 0 | C | A | 35.7% | 137.1 / 36.0 | 70 | intergenic (+318/+1055) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 1,819,313 | 0 | G | A | 35.5% | 106.8 / 23.4 | 62 | intergenic (‑119/+84) | ves/spy | environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy |
| * | NZ_CP009273 | 4,492,581 | 0 | A | C | 35.3% | 131.0 / 12.5 | 68 | L229R (CTG→CGG) | insG | IS4‑like element IS4 family transposase |
| * | NZ_CP009273 | 2,369,318 | 0 | A | C | 35.2% | 133.9 / 10.7 | 71 | W42G (TGG→GGG) | menC | o‑succinylbenzoate synthase |
| * | NZ_CP009273 | 5,123 | 0 | C | A | 35.1% | 119.1 / 21.4 | 57 | intergenic (+103/‑111) | thrC/yaaX | threonine synthase/DUF2502 domain‑containing protein |
| * | NZ_CP009273 | 3,171,107 | 0 | C | A | 34.8% | 123.9 / 25.5 | 69 | E55* (GAG→TAG) | nudF | ADP‑ribose diphosphatase |
| * | NZ_CP009273 | 5,162 | 0 | T | A | 34.5% | 112.5 / 17.7 | 58 | intergenic (+142/‑72) | thrC/yaaX | threonine synthase/DUF2502 domain‑containing protein |
| * | NZ_CP009273 | 2,331,202 | 0 | A | C | 33.9% | 107.6 / 10.0 | 57 | G566G (GGT→GGG) | gyrA | DNA topoisomerase (ATP‑hydrolyzing) subunit A |
| * | NZ_CP009273 | 2,852,805 | 0 | T | G | 33.9% | 106.4 / 11.5 | 59 | V785G (GTT→GGT) | mutS | DNA mismatch repair protein MutS |
| * | NZ_CP009273 | 2,033,556 | 0 | C | G | 33.3% | 95.5 / 14.4 | 61 | L200V (CTG→GTG) | msrP | protein‑methionine‑sulfoxide reductase catalytic subunit MsrP |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 42 (0.510) | 35 (0.420) | 32/496 | 4.1 | 42.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 52 (0.630) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | = 3416707 | 55 (0.670) | 3 (0.140) +184 bp |
3/128 | 4.5 | 17.4% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416709 = | 55 (0.670) | intergenic (+156/+75) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 47 (0.570) | 28 (0.350) +AATTCC |
27/484 | 4.9 | 32.9% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 70 (0.850) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 45 (0.550) | 4 (0.080) +93 bp |
4/310 | 10.3 | 11.3% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 55 (0.670) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 360286 | 54 (0.650) | 10 (0.120) +AATTC |
8/486 | 12.0 | 17.1% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 45 (0.550) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 47 (0.570) | 8 (0.100) +AATTCC |
8/484 | 12.0 | 11.9% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 74 (0.900) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 45 (0.550) | 4 (0.050) +GAATTAATTCC |
4/474 | 14.5 | 6.8% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 70 (0.850) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 692117 | 64 (0.780) | 4 (0.050) +GT |
4/492 | 14.9 | 5.8% | intergenic (‑45/+3) | BW25113_RS03445/BW25113_RS03450 | tRNA‑Gln/tRNA‑Met |
| ? | NZ_CP009273 | 692513 = | 66 (0.800) | noncoding (77/77 nt) | BW25113_RS03470 | tRNA‑Met | |||||