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 45 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 | 52.6% | ‑2.3 / 12.9 | 19 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.5% | 1.1 / 153.0 | 109 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 50.0% | 14.8 / 11.1 | 29 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 48.5% | 12.6 / 11.2 | 36 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 47.7% | 48.1 / 186.4 | 130 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 47.0% | 87.1 / 201.2 | 151 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 955,153 | 0 | T | C | 44.8% | 11.1 / 32.4 | 29 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,149 | 0 | A | G | 44.4% | 11.7 / 28.3 | 27 | intergenic (+103/‑210) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,151 | 0 | G | A | 42.9% | 15.5 / 28.3 | 28 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,155 | 0 | C | T | 42.9% | 15.0 / 28.2 | 29 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 42.3% | 13.7 / 14.7 | 30 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 955,152 | 0 | T | A | 41.4% | 14.2 / 31.8 | 29 | intergenic (+106/‑207) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 3,989,361 | 0 | A | C | 37.5% | 87.6 / 27.5 | 64 | T627P (ACC→CCC) | oplA | 5‑oxoprolinase A |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 34.9% | 29.7 / 14.1 | 45 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,275,725 | 0 | G | C | 34.0% | 102.1 / 12.3 | 53 | intergenic (+44/+62) | rlmG/PP_4649 | ribosomal RNA large subunit methyltransferase G/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,462,375 | 0 | T | G | 33.7% | 103.3 / 30.2 | 111 | intergenic (+18/‑22) | PP_4795/holA | lipoprotein/DNA polymerase III subunit delta |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 33.0% | 95.1 / 28.6 | 117 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,340,188 | 0 | A | G | 31.8% | 26.7 / 15.0 | 22 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947_CJ‑RC | 4,340,189 | 0 | C | T | 31.8% | 31.3 / 13.4 | 22 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947_CJ‑RC | 4,340,190 | 0 | A | G | 31.8% | 28.4 / 12.6 | 22 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 51 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 64 (0.750) | 12 (0.160) | 11/252 | 7.9 | 30.3% | 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 | 3 (0.040) | 15 (0.180) +GCC |
13/286 | 8.1 | 83.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 43 (0.500) | 12 (0.150) | 12/276 | 8.2 | 19.1% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 61 (0.760) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 11 (0.140) | 10/268 | 8.8 | 35.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 36 (0.460) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 47 (0.550) | 11 (0.130) | 10/282 | 9.3 | 19.9% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 43 (0.520) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2837075 | 16 (0.190) | 9 (0.110) | 9/268 | 9.3 | 49.1% | intergenic (‑27/+156) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947_CJ‑RC | 2837172 = | 4 (0.050) | intergenic (‑124/+59) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947_CJ‑RC | = 5455953 | 4 (0.050) | 3 (0.050) +48 bp |
3/196 | 10.5 | 15.0% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947_CJ‑RC | 5548441 = | 47 (0.550) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 5226203 = | 8 (0.090) | 3 (0.050) +48 bp |
3/196 | 10.5 | 14.0% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947_CJ‑RC | 5548441 = | 47 (0.550) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 4075618 = | 5 (0.060) | 3 (0.050) +48 bp |
3/196 | 10.5 | 14.7% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947_CJ‑RC | 5548441 = | 47 (0.550) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947_CJ‑RC | 3828180 = | 4 (0.050) | 3 (0.050) +48 bp |
3/196 | 10.5 | 15.0% | intergenic (‑204/+155) | PP_3381/PP_3382 | transposase/gluconate 2‑dehydrogenase cytochrome c subunit |
| ? | NC_002947_CJ‑RC | 5548441 = | 47 (0.550) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||