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 414 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% | 50.2 / 18.5 | 52 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 2,354,816 | 0 | A | C | 47.3% | 89.4 / 14.2 | 74 | G26G (GGT→GGG) | rhmD | L‑rhamnonate dehydratase |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 46.8% | 19.4 / 19.9 | 48 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 3,806,632 | 0 | C | T | 42.9% | 49.5 / 20.8 | 50 | S181L (TCG→TTG) | coaBC | bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 42.6% | 85.2 / 18.9 | 54 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 3,856,028 | 0 | A | G | 41.8% | 66.5 / 21.9 | 67 | pseudogene (936/1617 nt) | BW25113_RS19145 | PTS sugar transporter subunit IIB |
| * | NZ_CP009273 | 1,009,475 | 0 | A | G | 40.8% | 197.4 / 47.4 | 128 | E254G (GAA→GGA) | pqiB | intermembrane transport protein PqiB |
| * | NZ_CP009273 | 2,943,560 | 0 | T | G | 39.6% | 152.7 / 28.4 | 91 | G320G (GGT→GGG) | argA | amino‑acid N‑acetyltransferase |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 39.1% | 101.5 / 22.6 | 70 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 782,311 | 0 | A | C | 38.6% | 305.6 / 36.0 | 158 | G247G (GGT→GGG) | gpmA | 2,3‑diphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NZ_CP009273 | 1,009,484 | 0 | A | G | 38.5% | 206.8 / 62.4 | 131 | D257G (GAT→GGT) | pqiB | intermembrane transport protein PqiB |
| * | NZ_CP009273 | 1,257,298 | 0 | T | G | 38.3% | 155.7 / 15.0 | 81 | T12P (ACC→CCC) | prs | ribose‑phosphate diphosphokinase |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 38.2% | 92.1 / 51.2 | 68 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 1,995,399 | 0 | A | C | 38.0% | 134.6 / 13.6 | 71 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 3,344,203 | 0 | A | C | 37.7% | 149.1 / 22.4 | 77 | L728V (TTA→GTA) | arcB | aerobic respiration two‑component sensor histidine kinase ArcB |
| * | NZ_CP009273 | 4,526,014 | 0 | A | T | 37.2% | 107.6 / 63.2 | 78 | intergenic (+166/+102) | yjhR/BW25113_RS26295 | helicase YjhR/HNH endonuclease |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 37.0% | 116.3 / 26.1 | 73 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 36.4% | 204.3 / 46.0 | 107 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 1,170,082 | 0 | G | A | 36.4% | 111.6 / 17.9 | 67 | F180F (TTC→TTT) | ycfT | acyltransferase family protein |
| * | NZ_CP009273 | 1,155,293 | 0 | A | G | 36.2% | 141.0 / 20.3 | 80 | I572T (ATC→ACC) | fhuE | ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE |
| 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 | = 3416707 | 74 (0.720) | 6 (0.260) +191 bp |
6/114 | 3.4 | 26.1% | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 3416716 = | 76 (0.740) | intergenic (+163/+68) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | 52 (0.510) | 46 (0.450) | 41/496 | 4.4 | 50.0% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 40 (0.390) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 55 (0.540) | 32 (0.320) +AATTCC |
28/484 | 7.1 | 33.4% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 76 (0.740) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 692197 | 98 (0.950) | 17 (0.240) | 16/340 | 7.3 | 15.7% | intergenic (‑1/+15) | BW25113_RS03450/BW25113_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NZ_CP009273 | 692591 = | 115 (1.640) | intergenic (‑2/+378) | BW25113_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP009273 | = 360286 | 41 (0.400) | 19 (0.190) +AATTC |
18/486 | 10.4 | 25.9% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 70 (0.680) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 70 (0.680) | 4 (0.060) +93 bp |
4/310 | 13.1 | 8.2% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416707 | 74 (0.720) | intergenic (+154/+77) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 3541908 | 75 (0.730) | 5 (0.050) +23 bp |
5/450 | 16.5 | 6.6% | coding (1522/2085 nt) | malQ | 4‑alpha‑glucanotransferase |
| ? | NZ_CP009273 | 3541932 = | 80 (0.780) | coding (1498/2085 nt) | malQ | 4‑alpha‑glucanotransferase | |||||
| * | ? | NZ_CP009273 | 360104 = | 55 (0.540) | 7 (0.070) +AATTCC |
6/484 | 16.6 | 9.5% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 82 (0.800) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 3416618 = | 70 (0.680) | 5 (0.050) +GAATTAATTCC |
5/474 | 17.2 | 6.7% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | 4161677 = | 76 (0.740) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 1406156 = | 92 (0.900) | 4 (0.040) | 4/444 | 17.2 | 4.3% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NZ_CP009273 | = 1429215 | 94 (1.020) | intergenic (‑552/+227) | BW25113_RS25575/uspF | YnaM/YnfT family protein/universal stress protein UspF | |||||