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 234 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 40.5% | 161.2 / 64.3 | 121 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 4,091,435 | 0 | T | G | 40.4% | 171.1 / 22.3 | 109 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter |
| * | NZ_CP009273 | 4,277,638 | 0 | G | A | 38.2% | 111.0 / 33.0 | 76 | intergenic (‑339/‑54) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NZ_CP009273 | 2,380,341 | 0 | G | A | 37.3% | 92.2 / 44.2 | 68 | intergenic (+31/‑72) | yfbL/yfbM | M28 family metallopeptidase/YfbM family protein |
| * | NZ_CP009273 | 1,817,694 | 0 | C | T | 37.3% | 91.5 / 26.9 | 59 | intergenic (+152/‑78) | nadE/cho | ammonia‑dependent NAD(+) synthetase/excinuclease Cho |
| * | NZ_CP009273 | 4,036,390 | 0 | A | G | 36.7% | 102.8 / 10.4 | 60 | N206D (AAT→GAT) | srkA | stress response kinase SrkA |
| * | NZ_CP009273 | 4,277,647 | 0 | T | A | 36.0% | 118.2 / 40.5 | 75 | intergenic (‑348/‑45) | acs/nrfA | acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit |
| * | NZ_CP009273 | 2,089,571 | 0 | A | G | 35.8% | 156.7 / 25.3 | 96 | I83V (ATT→GTT) | hisF | imidazole glycerol phosphate synthase subunit HisF |
| * | NZ_CP009273 | 3,659,017 | 0 | C | A | 34.4% | 268.5 / 41.4 | 121 | V52L (GTA→TTA) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 2,897,074 | 0 | G | A | 33.9% | 177.6 / 70.6 | 109 | intergenic (+341/+1032) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 1,817,685 | 0 | C | G | 33.3% | 113.2 / 19.1 | 60 | intergenic (+143/‑87) | nadE/cho | ammonia‑dependent NAD(+) synthetase/excinuclease Cho |
| * | NZ_CP009273 | 2,503,359 | 0 | A | C | 33.3% | 185.0 / 13.1 | 90 | D84A (GAC→GCC) | yfeO | ion channel protein |
| * | NZ_CP009273 | 2,897,051 | 0 | C | A | 33.0% | 218.2 / 57.2 | 106 | intergenic (+318/+1055) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 2,221,718 | 0 | G | C | 32.7% | 77.5 / 13.4 | 53 | pseudogene (520/1436 nt) | mdtQ | multidrug resistance outer membrane protein MdtQ |
| * | NZ_CP009273 | 2,428,361 | 0 | T | G | 32.4% | 160.8 / 11.3 | 75 | Y252S (TAC→TCC) | truA | tRNA pseudouridine(38‑40) synthase TruA |
| * | NZ_CP009273 | 3,126,661 | 0 | T | G | 32.2% | 190.8 / 10.9 | 88 | H219P (CAC→CCC) | yghS | dTMP kinase |
| * | NZ_CP009273 | 3,199,805 | 0 | C | A | 32.1% | 103.2 / 20.5 | 83 | intergenic (‑190/‑17) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 3,941,210 | 0 | C | T | 32.1% | 154.0 / 36.1 | 81 | E40K (GAA→AAA) | hdfR | HTH‑type transcriptional regulator HdfR |
| * | NZ_CP009273 | 3,977,450 | 0 | T | C | 32.1% | 209.8 / 19.9 | 107 | F378S (TTC→TCC) | aslB | anaerobic sulfatase maturase |
| * | NZ_CP009273 | 2,428,342 | 0 | A | G | 31.9% | 126.2 / 16.9 | 74 | L258L (CTT→CTC) | truA | tRNA pseudouridine(38‑40) synthase TruA |
| 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 | = 2940826 | 47 (0.440) | 3 (0.040) | 3/328 | 14.4 | 6.9% | intergenic (+4/‑30) | BW25113_RS14635/BW25113_RS14640 | tRNA‑Met/tRNA‑Met |
| ? | NZ_CP009273 | 2941047 = | 50 (0.700) | intergenic (+5/+69) | BW25113_RS14645/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC | |||||
| * | ? | NZ_CP009273 | 4532499 = | 117 (1.080) | 7 (0.070) | 7/476 | 15.4 | 5.6% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 123 (1.180) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | = 4532507 | 118 (1.090) | 6 (0.060) | 6/476 | 16.1 | 4.8% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 123 (1.180) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 270430 = | NA (NA) | 3 (0.030) | 3/488 | 18.8 | NA | coding (363/981 nt) | BW25113_RS01325 | IS5‑like element IS5 family transposase |
| ? | NZ_CP009273 | 270448 = | NA (NA) | coding (345/981 nt) | BW25113_RS01325 | IS5‑like element IS5 family transposase | |||||
| * | ? | NZ_CP009273 | = 4059916 | 103 (0.950) | 3 (0.030) | 3/492 | 18.9 | 2.9% | coding (639/1386 nt) | yihP | MFS transporter |
| ? | NZ_CP009273 | = 4059924 | 100 (0.930) | coding (631/1386 nt) | yihP | MFS transporter | |||||
| * | ? | NZ_CP009273 | = 91066 | 73 (0.680) | 3 (0.030) | 3/492 | 18.9 | 3.9% | coding (1414/1488 nt) | murE | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| ? | NZ_CP009273 | = 91082 | 75 (0.700) | coding (1430/1488 nt) | murE | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase | |||||