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 36 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 | 4,158,471 | 0 | A | C | 61.5% | ‑1.1 / 24.3 | 42 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 56.4% | ‑4.0 / 19.8 | 41 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.6% | 30.2 / 163.5 | 117 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.1% | 10.9 / 159.9 | 118 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑5.6 / 10.7 | 10 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,442,726 | 0 | A | C | 44.4% | 20.5 / 12.2 | 38 | intergenic (‑89/+49) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 41.2% | 82.3 / 128.6 | 120 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 38.2% | 72.3 / 91.0 | 90 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 38.1% | 32.5 / 14.3 | 46 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,296,567 | 0 | G | T | 36.0% | 27.2 / 10.5 | 25 | intergenic (‑320/‑246) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 35.9% | 33.6 / 11.0 | 40 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 34.3% | 139.9 / 103.0 | 100 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 34.1% | 98.4 / 81.1 | 88 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 33.3% | 132.4 / 108.6 | 103 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,530,133 | 0 | T | A | 30.0% | 21.7 / 11.1 | 20 | intergenic (+32/‑136) | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 29.6% | 158.5 / 83.8 | 109 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 29.6% | 52.5 / 15.6 | 27 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 27.8% | 102.1 / 12.2 | 56 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 27.6% | 44.9 / 12.6 | 29 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,035,987 | 0 | G | C | 27.1% | 114.3 / 13.5 | 59 | Q10E (CAA→GAA) | PP_5477 | hypothetical 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 = | 10 (0.130) | 15 (0.250) | 14/222 | 5.2 | 33.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 52 (0.880) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.080) | 16 (0.220) | 14/268 | 6.7 | 33.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 57 (0.800) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 16 (0.210) +GCC |
14/286 | 7.2 | 84.5% | 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 | = 2957080 | 43 (0.550) | 13 (0.170) | 13/282 | 7.5 | 22.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 48 (0.640) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.030) | 16 (0.210) +CGGG |
12/284 | 7.9 | 89.2% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.030) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 59 (0.760) | 12 (0.160) | 11/276 | 8.1 | 15.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 75 (1.020) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 6 (0.080) | 8 (0.110) | 8/278 | 9.6 | 47.5% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 12 (0.160) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | 5762219 = | 36 (0.460) | 4 (0.070) | 4/228 | 10.4 | 15.3% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | 5762311 = | 16 (0.260) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947_CJ‑RC | = 3968879 | NA (NA) | 6 (0.080) | 6/278 | 10.8 | 9.2% | coding (1007/1179 nt) | PP_3498 | transposase |
| ? | NC_002947_CJ‑RC | 3968942 = | 62 (0.800) | coding (1070/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947_CJ‑RC | = 2050595 | 22 (0.280) | 3 (0.050) | 3/218 | 10.8 | 14.5% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2050631 | 19 (0.330) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||