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 263 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 681,493 | 0 | C | A | 52.4% | 13.0 / 29.5 | 21 | S211S (TCG→TCT) | gltJ | glutamate/aspartate ABC transporter permease GltJ |
| * | NZ_CP009273 | 284,093 | 0 | A | C | 42.4% | 71.5 / 16.6 | 59 | T532P (ACC→CCC) | yagH | glycoside hydrolase family 43 protein |
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 40.7% | 75.4 / 13.6 | 55 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 1,995,399 | 0 | A | C | 40.3% | 139.0 / 18.6 | 77 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 39.4% | 137.5 / 42.5 | 95 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 1,995,392 | 0 | G | A | 38.5% | 104.8 / 37.0 | 78 | intergenic (‑122/+199) | fliA/fliC | RNA polymerase sigma factor FliA/H48 family flagellin FliC |
| * | NZ_CP009273 | 3,394,818 | 0 | T | C | 37.9% | 138.4 / 28.0 | 88 | D625G (GAT→GGT) | csrD | RNase E specificity factor CsrD |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 37.8% | 127.0 / 32.4 | 74 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 2,897,051 | 0 | C | A | 37.5% | 139.9 / 45.3 | 80 | intergenic (+318/+1055) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 748,581 | 0 | T | A | 37.4% | 159.3 / 37.3 | 91 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 2,476,740 | 0 | C | A | 36.1% | 180.6 / 31.7 | 97 | A27S (GCG→TCG) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NZ_CP009273 | 2,221,768 | 0 | T | C | 35.3% | 80.0 / 10.5 | 51 | pseudogene (470/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 1,392,087 | 0 | T | C | 35.1% | 127.8 / 20.0 | 75 | I265V (ATT→GTT) | uspE | universal stress protein UspE |
| * | NZ_CP009273 | 3,941,210 | 0 | C | T | 34.8% | 151.6 / 39.1 | 89 | E40K (GAA→AAA) | hdfR | HTH‑type transcriptional regulator HdfR |
| * | NZ_CP009273 | 949,844 | 0 | C | T | 34.2% | 84.5 / 27.1 | 80 | A27T (GCA→ACA) | focA | formate transporter FocA |
| * | NZ_CP009273 | 1,240,690 | 0 | G | T | 34.1% | 175.4 / 29.5 | 91 | L25F (TTG→TTT) | BW25113_RS06225 | protein YcgY |
| * | NZ_CP009273 | 748,577 | 0 | C | A | 34.0% | 194.4 / 23.4 | 95 | intergenic (‑326/+64) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 2,476,733 | 0 | G | A | 34.0% | 183.2 / 36.2 | 100 | S29L (TCA→TTA) | emrK | multidrug efflux MFS transporter periplasmic adaptor subunit EmrK |
| * | NZ_CP009273 | 2,221,701 | 0 | T | G | 33.9% | 93.5 / 10.5 | 56 | pseudogene (537/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 4,526,014 | 0 | A | T | 33.8% | 117.3 / 44.3 | 71 | intergenic (+166/+102) | yjhR/BW25113_RS26295 | helicase YjhR/HNH endonuclease |
| 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 | 1203246 = | 75 (0.750) | 22 (0.230) | 21/464 | 8.4 | 23.9% | coding (290/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | 1205075 = | 70 (0.750) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 77 (0.770) | 19 (0.200) | 19/464 | 9.1 | 21.5% | coding (305/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | = 1205058 | 67 (0.710) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | 4532499 = | 139 (1.390) | 9 (0.090) | 9/478 | 14.0 | 6.5% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 123 (1.270) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 139 (1.390) | 5 (0.050) | 5/478 | 16.8 | 3.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 123 (1.270) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 1205074 | 75 (0.750) | 3 (0.030) | 3/466 | 18.2 | 4.1% | coding (41/540 nt) | BW25113_RS06005 | phage tail protein |
| ? | NZ_CP009273 | 2465376 = | 70 (0.740) | coding (283/636 nt) | BW25113_RS12285 | hypothetical protein | |||||