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 23 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 | 1,327,121 | 0 | C | T | 58.1% | ‑6.0 / 155.5 | 129 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.1% | ‑4.0 / 123.2 | 91 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,544,404 | 0 | T | G | 50.0% | ‑5.4 / 10.6 | 14 | V403G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 46.9% | 47.9 / 154.6 | 111 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,952,675 | 0 | T | G | 42.9% | 2.4 / 15.2 | 22 | intergenic (‑122/+35) | fliL/fliK | flagellar protein FliL/flagellar hook‑length control protein FliK |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 41.5% | 22.6 / 18.9 | 41 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 41.4% | 17.7 / 10.6 | 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 39.1% | 15.4 / 11.6 | 24 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,655,775 | 0 | T | G | 38.9% | 19.8 / 10.2 | 19 | intergenic (‑61/+100) | PP_4961/PP_4962 | lipoprotein/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,076,087 | 0 | G | T | 32.0% | 16.9 / 10.0 | 29 | intergenic (‑35/+39) | PP_2685/PP_2686 | hypothetical protein/transglutaminase domain‑containing protein |
| * | NC_002947_CJ‑RC | 697,123 | 0 | G | T | 31.0% | 48.0 / 10.1 | 29 | intergenic (+50/‑701) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 29.4% | 22.4 / 12.4 | 17 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 27.3% | 25.8 / 15.5 | 22 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 26.3% | 19.7 / 12.4 | 19 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 26.2% | 108.4 / 39.5 | 61 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,123,539 | 0 | C | G | 25.5% | 88.9 / 14.0 | 47 | R305P (CGC→CCC) | PP_4508 | AraC family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,438,934 | 0 | C | A | 23.5% | 104.8 / 16.5 | 51 | A246S (GCC→TCC) | yveA | aspartate‑proton symporter |
| * | NC_002947_CJ‑RC | 5,658,451 | 0 | C | A | 22.9% | 61.9 / 15.5 | 36 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 5,066,466 | 0 | G | T | 22.4% | 139.5 / 14.0 | 58 | D78E (GAC→GAA) | PP_4461 | MFS transporter |
| * | NC_002947_CJ‑RC | 3,537,948 | 0 | C | A | 22.2% | 116.4 / 12.2 | 54 | Q118K (CAA→AAA) | PP_3126 | polysaccharide biosynthesis/export protein |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 19 (0.370) | 14/220 | 3.9 | 47.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 38 (0.750) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 18 (0.270) +GCC |
15/284 | 5.1 | 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 | = 4809882 | 9 (0.130) | 13 (0.210) | 12/266 | 5.7 | 28.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 57 (0.930) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 64 (0.950) | 10 (0.160) | 9/274 | 7.0 | 14.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 54 (0.850) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 10 (0.150) +CGGG |
9/282 | 7.2 | 91.1% | 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 | = 1419549 | 10 (0.150) | 16 (0.240) | 9/284 | 7.3 | 51.8% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 20 (0.300) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 9 (0.130) | 8 (0.130) | 8/276 | 7.5 | 50.7% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 7 (0.110) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 39 (0.580) | 8 (0.120) | 8/280 | 7.6 | 19.1% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 30 (0.460) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 9 (0.130) | 12 (0.190) | 7/266 | 7.8 | 28.1% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 53 (0.860) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 5916972 = | 21 (0.310) | 5 (0.090) | 5/234 | 8.0 | 26.4% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | 5917068 = | 11 (0.200) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||