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 33 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 | 697,094 | 0 | A | G | 61.9% | ‑5.3 / 15.5 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,338,611 | 0 | A | T | 59.3% | 7.4 / 23.0 | 28 | intergenic (+124/+18) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 4,338,608 | 0 | G | T | 55.6% | 11.7 / 31.7 | 28 | intergenic (+121/+21) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 54.9% | 17.4 / 164.5 | 123 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,466,841 | 0 | T | G | 52.6% | 7.0 / 20.9 | 21 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.5% | 26.2 / 153.0 | 110 | 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 | 49.5% | 2.5 / 149.5 | 103 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 48.3% | 1.4 / 11.6 | 29 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 38.1% | 21.3 / 24.6 | 21 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 38.1% | 15.9 / 24.6 | 21 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,248 | 0 | A | T | 38.1% | 15.6 / 20.1 | 21 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 38.1% | 18.0 / 25.8 | 21 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 37.1% | 45.3 / 10.3 | 37 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 955,155 | 0 | C | T | 36.8% | 14.7 / 12.3 | 19 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 5,754,532 | 0 | G | C | 36.1% | 46.8 / 12.4 | 36 | intergenic (‑155/‑316) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 955,153 | 0 | T | C | 33.3% | 13.7 / 10.2 | 20 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 1,013,255 | 0 | A | T | 33.3% | 21.0 / 16.3 | 21 | intergenic (+83/+48) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 5,754,561 | 0 | A | C | 30.8% | 21.9 / 11.6 | 30 | intergenic (‑184/‑287) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 1,013,234 | 0 | C | A | 30.0% | 36.4 / 14.5 | 20 | intergenic (+62/+69) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,235 | 0 | A | T | 30.0% | 24.1 / 12.8 | 20 | intergenic (+63/+68) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 45 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 3 (0.050) | 15 (0.300) | 10/220 | 5.5 | 56.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 21 (0.420) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 37 (0.560) | 14 (0.220) | 14/280 | 5.6 | 27.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 38 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 3 (0.050) | 12 (0.220) | 10/238 | 6.0 | 43.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 29 (0.530) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.020) | 13 (0.200) +GCC |
11/284 | 6.8 | 93.0% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.020) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.060) | 7 (0.120) | 6/250 | 8.3 | 32.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 26 (0.450) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5455953 | 2 (0.030) | 3 (0.070) +48 bp |
3/194 | 8.4 | 16.0% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947_CJ‑RC | 5548441 = | 45 (0.680) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 5226203 = | 0 (0.000) | 3 (0.070) +48 bp |
3/194 | 8.4 | 16.6% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947_CJ‑RC | 5548441 = | 45 (0.680) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 4075618 = | 3 (0.050) | 3 (0.070) +48 bp |
3/194 | 8.4 | 15.7% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947_CJ‑RC | 5548441 = | 45 (0.680) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 3828180 = | 2 (0.030) | 3 (0.070) +48 bp |
3/194 | 8.4 | 16.0% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947_CJ‑RC | 5548441 = | 45 (0.680) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 2939258 = | 3 (0.050) | 3 (0.070) +48 bp |
3/194 | 8.4 | 15.7% | intergenic (‑204/+236) | PP_2570/PP_2572 | transposase/hypothetical protein |
| ? | NC_002947_CJ‑RC | 5548441 = | 45 (0.680) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||