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 204 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,397,828 | 0 | A | T | 60.0% | ‑5.8 / 13.5 | 15 | L60L (CTT→CTA) ‡ | PP_3868 | group II intron‑encoding maturase |
| * | NC_002947 | 4,397,829 | 0 | A | T | 60.0% | ‑5.8 / 13.5 | 15 | L60H (CTT→CAT) ‡ | PP_3868 | group II intron‑encoding maturase |
| * | NC_002947 | 4,397,835 | 0 | C | G | 54.5% | ‑6.6 / 11.5 | 11 | R58P (CGG→CCG) | PP_3868 | group II intron‑encoding maturase |
| * | NC_002947 | 699,725 | 0 | A | G | 50.0% | 68.2 / inf | 484 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,332,076 | 0 | C | T | 47.6% | 363.8 / inf | 630 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,353,698 | 0 | A | G | 47.4% | 283.4 / inf | 606 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 46.7% | 228.7 / inf | 641 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,287,762 | 0 | T | G | 45.0% | 105.9 / inf | 318 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 1,018,201 | 0 | T | G | 43.9% | 159.5 / inf | 258 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 4,813,174 | 0 | A | C | 42.7% | 47.9 / 135.8 | 103 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,175 | 0 | A | G | 42.7% | 42.7 / 121.9 | 103 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 5,745,476 | 0 | A | T | 42.5% | 83.9 / 226.7 | 207 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 1,018,200 | 0 | A | T | 41.7% | 217.2 / inf | 283 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,549,480 | 0 | C | A | 41.4% | 274.6 / inf | 304 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,345,069 | 0 | G | C | 41.3% | 148.6 / 195.0 | 151 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,287,766 | 0 | G | C | 41.1% | 231.8 / inf | 292 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,287,767 | 0 | G | C | 41.1% | 213.6 / inf | 292 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,287,771 | 0 | C | A | 40.6% | 249.7 / inf | 303 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,345,074 | 0 | A | G | 40.6% | 119.2 / 152.0 | 141 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,345,076 | 0 | A | G | 40.4% | 117.6 / 150.4 | 138 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 994 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.460) | 63/184 | 3.4 | 47.1% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842111 | 72 (0.300) | intergenic (‑71/+112) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | 4813168 = | 79 (0.210) | 160 (0.550) | 73/218 | 3.8 | 47.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 290 (1.000) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.430) | 63/200 | 4.3 | 44.6% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842119 | 83 (0.310) | intergenic (‑79/+104) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.390) | 62/216 | 5.2 | 42.7% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842127 | 90 (0.310) | intergenic (‑87/+96) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | = 652785 | 382 (1.000) | 169 (0.510) | 72/248 | 5.3 | 50.7% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.370) | 64/232 | 5.7 | 40.3% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842135 | 105 (0.340) | intergenic (‑95/+88) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | = 4813173 | 59 (0.150) | 168 (0.480) | 70/264 | 6.3 | 52.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 253 (0.720) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.340) | 63/248 | 6.7 | 38.0% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842143 | 124 (0.380) | intergenic (‑103/+80) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.320) | 63/264 | 7.5 | 36.2% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842151 | 138 (0.390) | intergenic (‑111/+72) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | 2842056 = | 285 (0.740) | 113 (0.300) | 64/280 | 8.0 | 34.1% | intergenic (‑16/+167) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | = 2842159 | 160 (0.430) | intergenic (‑119/+64) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||