mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 526,792 | 0 | A | C | 50.0% | ‑5.9 / 20.3 | 18 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 50.0% | ‑1.2 / 27.6 | 18 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 47.1% | 1.3 / 19.3 | 17 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 1,736,100 | 0 | T | A | 31.6% | 16.8 / 16.2 | 19 | intergenic (+141/+21) | sodB/ydhP | superoxide dismutase, Fe/putative MFS transporter, inner membrane protein |
| * | NC_000913_3_pae_pgi | 2,375,483 | 0 | A | T | 29.4% | 22.6 / 12.0 | 17 | L160L (CTT→CTA) ‡ | menC | O‑succinylbenzoyl‑CoA synthase |
| * | NC_000913_3_pae_pgi | 2,375,484 | 0 | A | T | 29.4% | 23.5 / 11.8 | 17 | L160H (CTT→CAT) ‡ | menC | O‑succinylbenzoyl‑CoA synthase |
| * | NC_000913_3_pae_pgi | 1,736,097 | 0 | T | A | 28.6% | 22.5 / 15.6 | 21 | intergenic (+138/+24) | sodB/ydhP | superoxide dismutase, Fe/putative MFS transporter, inner membrane protein |
| * | NC_000913_3_pae_pgi | 3,781,051 | 0 | C | G | 27.8% | 29.9 / 11.6 | 18 | intergenic (+34/‑164) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | NC_000913_3_pae_pgi | 4,376,082 | 0 | A | T | 27.8% | 26.0 / 11.1 | 18 | intergenic (+123/‑53) | ecnB/sugE | entericidin B membrane lipoprotein/multidrug efflux system protein |
| * | NC_000913_3_pae_pgi | 3,156,590 | 0 | C | A | 27.3% | 45.4 / 12.1 | 22 | intergenic (+72/‑33) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| * | NC_000913_3_pae_pgi | 3,156,591 | 0 | T | G | 27.3% | 38.0 / 15.5 | 22 | intergenic (+73/‑32) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| * | NC_000913_3_pae_pgi | 3,183,350 | 0 | A | . | 23.5% | 41.0 / 10.4 | 17 | intergenic (+27/+463) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| * | NC_000913_3_pae_pgi | 3,183,345 | 1 | . | T | 22.2% | 36.6 / 14.5 | 18 | intergenic (+22/+468) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| * | NC_000913_3_pae_pgi | 4,519,764 | 1 | . | T | 20.0% | 49.0 / 14.1 | 20 | intergenic (‑180/+167) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 3328181 | 19 (1.100) | 4 (0.250) | 4/252 | 1.8 | 17.2% | intergenic (+98/+58) | yhbY/greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor |
| ? | NC_000913_3_pae_pgi | = 3328184 | 21 (1.310) | intergenic (+101/+55) | yhbY/greA | RNA binding protein associated with pre‑50S ribosomal subunits/transcript cleavage factor | |||||
| * | ? | NC_000913_3_pae_pgi | = 2892692 | 19 (1.100) | 4 (0.240) | 4/260 | 1.8 | 17.7% | coding (36/1272 nt) | ygcN | putative oxidoreductase |
| ? | NC_000913_3_pae_pgi | = 2892701 | 19 (1.150) | coding (45/1272 nt) | ygcN | putative oxidoreductase | |||||
| * | ? | NC_000913_3_pae_pgi | = 2641725 | 16 (0.920) | 4 (0.250) | 4/256 | 1.8 | 20.0% | coding (80/1119 nt) | ispG | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase |
| ? | NC_000913_3_pae_pgi | = 2641730 | 17 (1.040) | coding (75/1119 nt) | ispG | 1‑hydroxy‑2‑methyl‑2‑(E)‑butenyl 4‑diphosphate synthase | |||||
| * | ? | NC_000913_3_pae_pgi | 925564 = | 25 (1.440) | 4 (0.250) | 4/252 | 1.8 | 15.6% | intergenic (+24/+320) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | NC_000913_3_pae_pgi | 925596 = | 20 (1.250) | intergenic (+56/+288) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser | |||||
| * | ? | NC_000913_3_pae_pgi | = 4542860 | 17 (0.980) | 4 (0.240) | 4/266 | 1.9 | 17.5% | coding (486/549 nt) | fimA | major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_pae_pgi | = 4542880 | 21 (1.240) | coding (506/549 nt) | fimA | major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_pae_pgi | = 4162839 | 18 (1.040) | 3 (0.180) | 3/258 | 2.1 | 14.3% | coding (432/1101 nt) | trmA | tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase |
| ? | NC_000913_3_pae_pgi | = 4162849 | 19 (1.160) | coding (422/1101 nt) | trmA | tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase | |||||
| * | ? | NC_000913_3_pae_pgi | = 4124709 | 13 (0.750) | 4 (0.240) | 3/258 | 2.1 | 22.7% | coding (2102/2199 nt) | priA | Primosome factor n' (replication factor Y) |
| ? | NC_000913_3_pae_pgi | = 4124729 | 15 (0.910) | coding (2082/2199 nt) | priA | Primosome factor n' (replication factor Y) | |||||
| * | ? | NC_000913_3_pae_pgi | 3312700 = | 17 (0.980) | 4 (0.250) | 3/254 | 2.1 | 21.7% | coding (78/945 nt) | truB | tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase |
| ? | NC_000913_3_pae_pgi | 3312734 = | 13 (0.800) | coding (44/945 nt) | truB | tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase | |||||
| * | ? | NC_000913_3_pae_pgi | = 3167879 | 21 (1.210) | 3 (0.190) | 3/254 | 2.1 | 13.5% | coding (368/396 nt) | mqsA | antitoxin for MqsR toxin; transcriptional repressor |
| ? | NC_000913_3_pae_pgi | = 3167883 | 19 (1.170) | coding (364/396 nt) | mqsA | antitoxin for MqsR toxin; transcriptional repressor | |||||
| * | ? | NC_000913_3_pae_pgi | 1563562 = | 29 (1.670) | 4 (0.240) | 3/258 | 2.1 | 12.8% | coding (2172/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| ? | NC_000913_3_pae_pgi | 1563577 = | 27 (1.640) | coding (2157/2400 nt) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator | |||||