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 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 278,742 | 1 | . | A | 72.7% | 46.1 / 16.0 | 22 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 67.7% | 65.3 / 31.7 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 67.7% | 60.2 / 32.4 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 58.3% | 2.6 / 177.6 | 144 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.0% | 3.6 / 130.6 | 101 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.5% | 0.9 / 131.8 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,809,884 | 0 | A | G | 45.5% | ‑3.3 / 10.3 | 11 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 38.9% | 6.6 / 12.0 | 18 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 38.1% | 13.2 / 10.5 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 37.2% | 35.6 / 15.6 | 46 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,583,677 | 1 | . | G | 31.2% | 19.2 / 19.8 | 16 | intergenic (‑143/+28) | treSB/glgE | bifunctional trehalose synthase B/maltokinase/alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| * | NC_002947_CJ‑RC | 2,101,751 | 0 | A | C | 29.8% | 52.1 / 14.2 | 60 | L186R (CTG→CGG) | PP_1878 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,392,143 | 0 | T | G | 28.1% | 107.3 / 13.7 | 59 | intergenic (+529/‑193) | PP_4738/PP_mr56 | hypothetical protein/C4 ncRNA |
| * | NC_002947_CJ‑RC | 4,798,317 | 0 | G | C | 27.3% | 34.4 / 14.6 | 23 | intergenic (‑172/+46) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 26.1% | 47.0 / 13.7 | 23 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 6,007,797 | 0 | G | A | 26.1% | 74.5 / 15.5 | 47 | intergenic (+20/‑156) | PP_5259/ydcJ | LysR family transcriptional regulator/metalloprotein |
| * | NC_002947_CJ‑RC | 5,392,153 | 0 | C | G | 24.6% | 126.8 / 10.6 | 61 | intergenic (+539/‑183) | PP_4738/PP_mr56 | hypothetical protein/C4 ncRNA |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 24.1% | 166.8 / 51.1 | 87 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 24.1% | 65.1 / 18.5 | 29 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 24.1% | 67.1 / 16.2 | 29 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 19 (0.310) | 15/266 | 4.4 | 46.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 38 (0.610) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 12 (0.180) +CGGG |
11/282 | 6.0 | 100% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 8 (0.120) | 11 (0.200) | 8/238 | 6.2 | 38.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 28 (0.500) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 13 (0.220) | 8/250 | 6.5 | 34.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 45 (0.770) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 25 (0.370) | 9 (0.140) | 9/280 | 6.7 | 23.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 34 (0.520) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 337781 = | 20 (0.300) | 5 (0.090) | 5/234 | 7.5 | 24.3% | intergenic (‑31/+98) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947_CJ‑RC | 337865 = | 15 (0.270) | intergenic (‑115/+14) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 7 (0.110) +GCC |
7/284 | 7.7 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5433190 | 30 (0.440) | 7 (0.110) | 6/272 | 7.9 | 18.1% | intergenic (‑57/+104) | PP_4769/PP_4770 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 5433241 | 35 (0.550) | intergenic (‑108/+53) | PP_4769/PP_4770 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 38 (0.560) | 6 (0.090) | 6/274 | 8.0 | 12.4% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 49 (0.770) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 2236919 = | 32 (0.470) | 5 (0.080) | 5/258 | 8.1 | 17.4% | intergenic (+14/+114) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter |
| ? | NC_002947_CJ‑RC | 2237010 = | 19 (0.320) | intergenic (+105/+23) | uvrB/PP_1975 | uvrABC excinuclease protein B/EmrB/QacA family drug resistance transporter | |||||