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 42 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 | 1,070,246 | 1 | . | G | 63.3% | 49.1 / 37.2 | 30 | 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 | 63.3% | 48.1 / 37.5 | 30 | 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 | 61.1% | 0.9 / 10.0 | 19 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 60.8% | 10.0 / 146.6 | 130 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,712,090 | 0 | G | C | 53.8% | 2.3 / 12.8 | 13 | intergenic (+81/‑177) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 53.1% | 5.4 / 28.5 | 34 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,840,084 | 0 | T | G | 51.6% | 25.6 / 47.1 | 33 | intergenic (+16/+20) | PP_1646/PP_1647 | thioredoxin/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 48.3% | 8.1 / 12.2 | 32 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 47.1% | 16.7 / 144.7 | 102 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 44.1% | 87.8 / 184.9 | 143 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,987,264 | 0 | T | C | 42.1% | 2.7 / 18.3 | 21 | intergenic (+45/+44) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 41.9% | 9.9 / 12.5 | 34 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,987,259 | 0 | T | C | 38.1% | 9.8 / 18.8 | 22 | intergenic (+40/+49) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,270 | 0 | G | A | 38.1% | 12.0 / 17.4 | 21 | intergenic (+51/+38) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,257 | 0 | G | A | 36.4% | 15.3 / 16.9 | 22 | intergenic (+38/+51) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,262 | 0 | G | A | 36.4% | 16.8 / 16.9 | 22 | intergenic (+43/+46) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 5,987,251 | 0 | T | C | 35.0% | 13.9 / 15.1 | 21 | intergenic (+32/+57) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 955,149 | 0 | A | G | 33.3% | 37.1 / 20.3 | 31 | intergenic (+103/‑210) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 5,442,128 | 0 | G | C | 32.6% | 84.0 / 12.7 | 46 | R15G (CGG→GGG) | rluE | 23S rRNA pseudouridine(2457) synthase |
| * | NC_002947_CJ‑RC | 955,151 | 0 | G | A | 32.3% | 43.9 / 20.4 | 31 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| Marginal new junction evidence (lowest skew 10 of 69 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 8 (0.100) | 21 (0.340) | 16/218 | 4.4 | 44.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 47 (0.760) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 61 (0.750) | 14 (0.200) | 13/248 | 6.2 | 34.8% | 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 | = 5684230 | 2 (0.020) | 16 (0.200) +CGGG |
14/280 | 6.8 | 89.2% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 15 (0.190) +GCC |
14/282 | 6.8 | 93.9% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 13 (0.170) | 12/264 | 7.1 | 35.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 44 (0.590) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 11 (0.160) | 10/248 | 7.4 | 26.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 60 (0.850) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 33 (0.400) | 10 (0.130) | 10/278 | 8.3 | 21.8% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 40 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 50 (0.610) | 8 (0.100) | 8/272 | 9.0 | 13.2% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 58 (0.750) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5873104 | 30 (0.370) | 6 (0.090) | 5/230 | 9.4 | 21.4% | intergenic (+50/+84) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator |
| ? | NC_002947_CJ‑RC | = 5873139 | 20 (0.310) | intergenic (+85/+49) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator | |||||
| * | ? | NC_002947_CJ‑RC | 2794924 = | 63 (0.770) | 7 (0.090) | 7/284 | 9.9 | 10.6% | intergenic (+32/+80) | PP_2447/puuB | hypothetical protein/gamma‑glutamylputrescine oxidase |
| ? | NC_002947_CJ‑RC | 2794973 = | 56 (0.700) | intergenic (+81/+31) | PP_2447/puuB | hypothetical protein/gamma‑glutamylputrescine oxidase | |||||