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 39 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 | 1,070,246 | 2 | . | A | 73.7% | 69.5 / 32.0 | 38 | 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 | 1 | . | G | 68.8% | 49.8 / 31.1 | 38 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 53.6% | ‑6.0 / 17.1 | 29 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,466,846 | 0 | C | G | 52.6% | 5.1 / 16.7 | 19 | intergenic (‑21/+103) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 52.0% | 7.3 / 29.0 | 25 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.0% | 59.3 / 255.7 | 176 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 52.0% | ‑3.1 / 173.9 | 127 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑5.2 / 19.0 | 14 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,809,884 | 0 | A | G | 50.0% | ‑6.4 / 16.7 | 14 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 49.3% | 43.3 / 214.5 | 143 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 43.2% | 39.4 / 12.2 | 37 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 697,101 | 0 | C | G | 42.9% | 5.0 / 11.8 | 28 | intergenic (+28/‑723) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 42.9% | 13.3 / 12.7 | 31 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,809,890 | 0 | G | T | 41.7% | ‑0.3 / 12.2 | 12 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 5,442,133 | 0 | T | G | 39.7% | 66.9 / 21.3 | 64 | Q13P (CAG→CCG) | rluE | 23S rRNA pseudouridine(2457) synthase |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 36.9% | 106.5 / 17.6 | 68 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 35.9% | 95.6 / 33.2 | 116 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 35.5% | 14.4 / 13.6 | 31 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 33.3% | 44.4 / 17.0 | 43 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 33.3% | 28.5 / 12.9 | 22 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 62 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 10 (0.110) | 21 (0.300) | 16/220 | 5.5 | 39.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 57 (0.800) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 17 (0.190) +GCC |
17/284 | 7.2 | 94.5% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 37 (0.390) | 16 (0.180) | 15/280 | 7.8 | 30.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 37 (0.410) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 353066 | 20 (0.210) | 11 (0.130) | 10/272 | 9.6 | 40.9% | intergenic (+33/+85) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| ? | NC_002947_CJ‑RC | = 353120 | 13 (0.150) | intergenic (+87/+31) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 58 (0.620) | 8 (0.110) +29 bp |
7/232 | 9.8 | 21.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809865 | 16 (0.170) | intergenic (‑271/‑284) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 10 (0.110) | 12 (0.130) | 10/284 | 10.0 | 42.3% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 23 (0.250) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 80 (0.850) | 9 (0.100) | 9/274 | 10.2 | 10.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 78 (0.880) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 13 (0.140) +CGGG |
8/282 | 10.9 | 93.0% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809865 | 16 (0.170) | 5 (0.070) +29 bp |
5/232 | 11.0 | 11.4% | intergenic (‑271/‑284) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991784 | 81 (0.860) | intergenic (+263/‑283) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1114870 = | 42 (0.450) | 5 (0.060) | 5/240 | 11.3 | 12.9% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947_CJ‑RC | 1114946 = | 33 (0.430) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||