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 183 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 2,145,170 | 0 | G | T | 43.1% | 27.2 / 18.3 | 51 | intergenic (+43/+22) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 41.2% | 71.1 / 17.6 | 53 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 2,354,816 | 0 | A | C | 37.2% | 90.2 / 10.2 | 51 | G26G (GGT→GGG) | rhmD | L‑rhamnonate dehydratase |
| * | NZ_CP009273 | 4,036,353 | 0 | C | T | 35.7% | 45.7 / 10.4 | 42 | F193F (TTC→TTT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 2,145,167 | 0 | G | T | 35.3% | 38.5 / 17.6 | 51 | intergenic (+40/+25) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 4,594,167 | 0 | C | T | 35.2% | 133.2 / 39.2 | 92 | S64F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 4,594,161 | 0 | C | T | 34.4% | 130.8 / 36.5 | 92 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 383,643 | 0 | T | G | 34.0% | 187.5 / 16.6 | 94 | G131G (GGT→GGG) | tauD | taurine dioxygenase |
| * | NZ_CP009273 | 1,548,257 | 0 | T | G | 32.3% | 148.1 / 18.6 | 99 | Y557S (TAC→TCC) | maeA | malate dehydrogenase |
| * | NZ_CP009273 | 279,651 | 0 | A | G | 32.2% | 138.4 / 13.0 | 87 | E247G (GAG→GGG) | yagF | xylonate dehydratase YagF |
| * | NZ_CP009273 | 2,145,111 | 0 | C | A | 31.4% | 117.9 / 18.2 | 51 | A149E (GCA→GAA) | yegJ | DUF2314 domain‑containing protein |
| * | NZ_CP009273 | 3,524,799 | 0 | A | C | 31.3% | 351.0 / 19.4 | 150 | Y334D (TAT→GAT) | yhgE | DUF4153 domain‑containing protein |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 31.1% | 190.6 / 34.4 | 103 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 3,479,745 | 0 | G | A | 30.1% | 230.1 / 26.6 | 123 | A89A (GCG→GCA) | crp | cAMP‑activated global transcriptional regulator CRP |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 29.8% | 315.7 / 53.7 | 152 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 1,560,495 | 0 | C | T | 29.4% | 231.3 / 30.0 | 119 | T301T (ACG→ACA) | dosC | diguanylate cyclase DosC |
| * | NZ_CP009273 | 4,594,195 | 0 | A | G | 29.0% | 206.9 / 19.2 | 101 | G73G (GGA→GGG) | bglJ | DNA‑binding transcriptional activator BglJ |
| * | NZ_CP009273 | 2,360,878 | 0 | T | C | 29.0% | 127.7 / 12.7 | 69 | I110T (ATC→ACC) | arnC | undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase |
| * | NZ_CP009273 | 1,392,087 | 0 | T | C | 28.9% | 194.3 / 21.1 | 97 | I265V (ATT→GTT) | uspE | universal stress protein UspE |
| * | NZ_CP009273 | 2,145,143 | 0 | A | T | 28.8% | 120.3 / 11.1 | 55 | intergenic (+16/+49) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 360104 = | 78 (0.530) | 93 (0.640) | 70/496 | 3.1 | 54.7% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | 76 (0.520) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | 360104 = | 83 (0.570) | 76 (0.530) +AATTCC |
55/484 | 4.9 | 39.3% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4161677 = | 158 (1.080) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 1203246 = | 100 (0.690) | 38 (0.280) | 38/464 | 7.8 | 29.3% | coding (290/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | 1205075 = | 90 (0.660) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 110 (0.750) | 35 (0.260) | 33/464 | 9.1 | 26.6% | coding (305/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | = 1205058 | 90 (0.660) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | 3416618 = | 100 (0.690) | 5 (0.090) +152 bp |
5/192 | 10.8 | 11.5% | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA |
| ? | NZ_CP009273 | = 3416648 | 98 (0.670) | intergenic (+95/+136) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 360286 | 78 (0.530) | 22 (0.150) +AATTC |
19/486 | 14.6 | 20.2% | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 3416618 = | 100 (0.690) | intergenic (+65/+166) | yhdZ/rrf | amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | = 692197 | 83 (0.570) | 9 (0.090) | 9/340 | 15.0 | 11.3% | intergenic (‑1/+15) | BW25113_RS03450/BW25113_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NZ_CP009273 | 692591 = | 84 (0.840) | intergenic (‑2/+378) | BW25113_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP009273 | = 4532507 | 172 (1.180) | 12 (0.090) | 12/478 | 17.9 | 6.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 157 (1.120) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 172 (1.180) | 12 (0.090) | 12/478 | 17.9 | 6.9% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 158 (1.120) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 360104 = | 83 (0.570) | 15 (0.110) +AATTCC |
11/484 | 18.6 | 13.1% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | 4033989 = | 121 (0.830) | noncoding (111/116 nt) | rrf | 5S ribosomal RNA | |||||