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 31 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 | 3,466,841 | 0 | T | G | 56.5% | 0.5 / 20.9 | 24 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.4% | ‑5.3 / 22.2 | 25 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 51.7% | 0.6 / 19.2 | 33 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 51.2% | 59.2 / 252.4 | 171 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 48.5% | 5.2 / 13.4 | 33 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 45.0% | 38.1 / 144.9 | 109 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 41.5% | 108.7 / 172.4 | 142 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,226,245 | 0 | C | A | 38.9% | 17.4 / 10.3 | 18 | intergenic (‑246/+133) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 38.1% | 19.4 / 10.5 | 21 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 337,809 | 0 | A | G | 35.0% | 16.3 / 15.6 | 20 | intergenic (‑59/+70) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 33.3% | 50.6 / 11.3 | 51 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 32.7% | 93.9 / 11.2 | 56 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 4,338,600 | 0 | A | T | 32.0% | 27.7 / 15.4 | 25 | intergenic (+113/+29) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 245,405 | 0 | T | G | 31.8% | 75.6 / 10.6 | 46 | E123A (GAG→GCG) | PP_0195 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,658,456 | 0 | T | . | 31.6% | 37.8 / 18.9 | 20 | intergenic (‑96/+56) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 1,130,185 | 0 | C | A | 30.9% | 89.7 / 11.6 | 55 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,123,536 | 0 | A | C | 30.4% | 59.6 / 12.3 | 51 | L306R (CTG→CGG) | PP_4508 | AraC family transcriptional regulator |
| * | NC_002947_CJ‑RC | 337,816 | 1 | . | A | 29.4% | 34.0 / 19.9 | 17 | intergenic (‑66/+63) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 337,819 | 0 | A | C | 29.4% | 23.2 / 13.3 | 17 | intergenic (‑69/+60) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,658,451 | 0 | C | A | 28.6% | 25.3 / 14.7 | 21 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| Marginal new junction evidence (lowest skew 10 of 50 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.510) | 14 (0.180) | 13/280 | 7.4 | 23.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 51 (0.660) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 74 (0.930) | 11 (0.160) | 10/250 | 7.7 | 25.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 278744 | 24 (0.300) | 17 (0.230) | 11/268 | 7.9 | 36.9% | intergenic (‑239/+75) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 278792 | 36 (0.490) | intergenic (‑287/+27) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 14 (0.200) | 9/250 | 8.2 | 30.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 61 (0.890) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 12 (0.160) | 10/266 | 8.3 | 31.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 48 (0.660) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 13 (0.170) +GCC |
11/284 | 8.4 | 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 | = 5991586 | 48 (0.600) | 10 (0.130) | 10/274 | 8.5 | 15.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 64 (0.850) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 14 (0.180) +CGGG |
10/282 | 8.7 | 93.5% | 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 | = 2472115 | 41 (0.510) | 9 (0.120) | 9/276 | 9.0 | 13.0% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 82 (1.080) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 10 (0.130) | 8 (0.110) | 8/276 | 9.6 | 35.9% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 19 (0.250) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||