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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 67.7% | 59.4 / 29.0 | 32 | 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% | 57.0 / 30.1 | 32 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 55.6% | ‑4.9 / 15.9 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 53.8% | 5.1 / 17.1 | 22 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.6% | 23.6 / 134.2 | 100 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,666,787 | 0 | G | C | 46.4% | 24.4 / 10.6 | 28 | intergenic (‑59/‑212) | PP_1460/ffh | membrane protein/signal recognition particle GTPase subunit |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 45.2% | 42.7 / 113.3 | 84 | 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 | 42.7% | 40.3 / 89.8 | 75 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 41.9% | 20.9 / 10.8 | 31 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 30.2% | 74.4 / 11.4 | 73 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 29.3% | 74.8 / 15.8 | 76 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 661,666 | 0 | A | C | 25.0% | 72.6 / 10.2 | 40 | L430W (TTG→TGG) | PP_0569 | MATE efflux family protein |
| * | NC_002947_CJ‑RC | 5,541,380 | 0 | A | C | 23.5% | 86.7 / 15.3 | 51 | intergenic (+55/+66) | PP_4871/PP_4872 | lysine decarboxylase family protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,178,214 | 0 | G | C | 20.5% | 214.4 / 10.4 | 93 | V150V (GTG→GTC) | PP_1931 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,230,894 | 0 | G | C | 20.2% | 248.2 / 11.9 | 100 | intergenic (‑133/+43) | PP_4606/PP_4607 | ferric siderophore receptor/transmembrane sensor |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.080) | 14 (0.290) | 12/220 | 3.9 | 34.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 50 (1.040) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 44 (0.690) | 12 (0.220) | 10/250 | 5.2 | 38.8% | 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 | = 5558423 | 2 (0.030) | 13 (0.210) +GCC |
12/284 | 5.3 | 86.9% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 11 (0.190) | 10/266 | 5.6 | 31.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 42 (0.720) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 8 (0.150) | 7/250 | 6.4 | 19.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 61 (1.120) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 14 (0.220) | 7 (0.120) | 7/276 | 7.0 | 19.6% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 44 (0.730) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 661513 = | 40 (0.630) | 6 (0.110) +GGGCCGCATAGCGGCC |
6/258 | 7.1 | 22.3% | intergenic (+23/+104) | PP_0568/PP_0569 | hypothetical protein/MATE efflux family protein |
| ? | NC_002947_CJ‑RC | 5558424 = | 7 (0.110) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5455953 | 6 (0.090) | 3 (0.070) +48 bp |
3/194 | 7.2 | 15.2% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947_CJ‑RC | 5548441 = | 44 (0.690) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 5226203 = | 6 (0.090) | 3 (0.070) +48 bp |
3/194 | 7.2 | 15.2% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947_CJ‑RC | 5548441 = | 44 (0.690) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 4075618 = | 1 (0.020) | 3 (0.070) +48 bp |
3/194 | 7.2 | 16.6% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947_CJ‑RC | 5548441 = | 44 (0.690) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||