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 28 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 | 699,722 | 0 | A | G | 58.4% | 45.4 / 125.6 | 113 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 55.6% | ‑4.0 / 17.1 | 19 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,076,094 | 0 | T | A | 55.6% | ‑0.3 / 10.7 | 19 | intergenic (‑42/+32) | PP_2685/PP_2686 | hypothetical protein/transglutaminase domain‑containing protein |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 54.5% | 1.7 / 23.5 | 22 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 52.8% | 5.7 / 139.0 | 106 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 50.0% | ‑4.1 / 13.2 | 26 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑4.0 / 10.3 | 10 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,809,884 | 0 | A | G | 50.0% | ‑6.5 / 10.0 | 10 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,809,890 | 0 | G | T | 50.0% | ‑6.1 / 12.6 | 10 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.1% | 46.1 / 146.5 | 106 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,076,087 | 0 | G | T | 47.4% | 0.5 / 12.8 | 20 | intergenic (‑35/+39) | PP_2685/PP_2686 | hypothetical protein/transglutaminase domain‑containing protein |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 47.3% | 51.1 / 163.7 | 132 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 42.9% | 3.8 / 11.1 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 41.2% | 3.8 / 19.4 | 17 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 37.5% | 7.4 / 13.4 | 17 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 35.7% | 4.8 / 12.7 | 14 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 35.3% | 8.6 / 13.4 | 17 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,743,289 | 0 | C | A | 35.3% | 16.2 / 14.7 | 17 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 1,625,208 | 0 | A | C | 35.1% | 34.9 / 13.0 | 37 | intergenic (+31/+26) | PP_1425/nadB | hypothetical protein/L‑aspartate oxidase |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 31.9% | 168.0 / 72.9 | 92 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 20 (0.290) +GCC |
19/286 | 4.2 | 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 | 56 (0.810) | 18 (0.270) | 17/276 | 4.5 | 23.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 62 (0.950) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 22 (0.320) | 15 (0.220) | 15/282 | 5.2 | 35.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 34 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 11 (0.160) | 13 (0.200) | 13/278 | 5.7 | 57.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 9 (0.140) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 12 (0.170) | 15 (0.220) | 13/286 | 5.9 | 44.3% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 26 (0.380) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.100) | 13 (0.250) | 8/222 | 6.2 | 32.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 50 (0.950) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 53 (0.760) | 12 (0.200) | 10/252 | 6.2 | 34.4% | 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 | = 4809882 | 5 (0.070) | 11 (0.170) | 8/268 | 7.5 | 29.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 49 (0.770) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 14 (0.200) | 8 (0.120) | 8/278 | 7.7 | 24.5% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 36 (0.550) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 4898081 = | 18 (0.260) | 5 (0.080) | 5/250 | 8.6 | 25.4% | intergenic (+11/‑197) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947_CJ‑RC | 4898170 = | 14 (0.240) | intergenic (+100/‑108) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||