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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_tpiA | 1,544,021 | 1 | . | A | 72.7% | 77.3 / 26.8 | 33 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| * | NC_000913_3_pae_tpiA | 4,295,976 | 0 | C | T | 29.2% | 56.6 / 26.2 | 49 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence (lowest skew 10 of 89 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 4542606 | 27 (0.690) | 8 (0.220) | 8/268 | 3.5 | 21.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_pae_tpiA | = 4542902 | 32 (0.880) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_pae_tpiA | 1207790 = | 38 (0.970) | 7 (0.200) | 7/254 | 3.6 | 17.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | 1209619 = | 32 (0.930) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1207805 | 33 (0.850) | 7 (0.200) | 6/254 | 4.0 | 18.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | = 1209602 | 32 (0.930) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 2743678 | 42 (1.080) | 5 (0.130) | 5/272 | 4.7 | 11.1% | coding (54/483 nt) | yfiB | OM lipoprotein putative positive effector of YfiN activity |
| ? | NC_000913_3_pae_tpiA | = 2743679 | 40 (1.080) | coding (55/483 nt) | yfiB | OM lipoprotein putative positive effector of YfiN activity | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4341711 | 44 (1.130) | 4 (0.120) | 4/250 | 4.8 | 9.4% | intergenic (‑167/‑116) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding |
| ? | NC_000913_3_pae_tpiA | = 4341731 | 39 (1.150) | intergenic (‑187/‑96) | melR/melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding | |||||
| * | ? | NC_000913_3_pae_tpiA | 3587430 = | 40 (1.030) | 4 (0.110) | 4/266 | 5.1 | 8.9% | coding (684/744 nt) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic |
| ? | NC_000913_3_pae_tpiA | 3587464 = | 45 (1.240) | coding (650/744 nt) | ugpQ | glycerophosphodiester phosphodiesterase, cytosolic | |||||
| * | ? | NC_000913_3_pae_tpiA | 980791 = | 53 (1.360) | 4 (0.110) | 4/268 | 5.1 | 7.2% | intergenic (+5/‑256) | mukB/ldtD | chromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase |
| ? | NC_000913_3_pae_tpiA | 980813 = | 53 (1.450) | intergenic (+27/‑234) | mukB/ldtD | chromosome condensin MukBEF, ATPase and DNA‑binding subunit/murein L,D‑transpeptidase | |||||
| * | ? | NC_000913_3_pae_tpiA | 164559 = | 47 (1.210) | 4 (0.110) | 4/268 | 5.1 | 9.6% | intergenic (+25/‑171) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| ? | NC_000913_3_pae_tpiA | 289255 = | 31 (0.850) | intergenic (‑93/+46) | yagI/argF | CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4498162 | 19 (0.490) | 4 (0.110) | 4/274 | 5.2 | 19.4% | intergenic (+306/‑26) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA |
| ? | NC_000913_3_pae_tpiA | = 4498168 | 15 (0.400) | intergenic (+312/‑20) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | NC_000913_3_pae_tpiA | 4139396 = | 29 (0.740) | 4 (0.110) | 4/270 | 5.2 | 11.7% | coding (229/663 nt) | fsaB | fructose‑6‑phosphate aldolase 2 |
| ? | NC_000913_3_pae_tpiA | 4139434 = | 33 (0.900) | coding (191/663 nt) | fsaB | fructose‑6‑phosphate aldolase 2 | |||||