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 35 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 | 73.2% | 76.8 / 34.6 | 44 | 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 | 72.7% | 89.9 / 38.6 | 44 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 278,742 | 1 | . | A | 69.6% | 49.1 / 21.4 | 23 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| * | NC_002947_CJ‑RC | 4,353,299 | 0 | C | A | 63.6% | ‑0.4 / 10.0 | 11 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 61.9% | ‑4.0 / 12.3 | 21 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 58.8% | ‑3.9 / 11.5 | 20 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 55.0% | ‑5.0 / 18.1 | 20 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,842,821 | 0 | T | G | 50.0% | 2.6 / 13.5 | 32 | E658A (GAG→GCG) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 47.0% | 28.0 / 158.6 | 117 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 46.6% | 90.8 / 195.7 | 148 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 45.5% | 70.1 / 196.6 | 145 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,809,890 | 0 | G | T | 45.5% | ‑0.5 / 11.9 | 11 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 44.5% | 42.0 / 157.1 | 129 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 6,000,021 | 0 | G | T | 40.6% | 38.7 / 20.1 | 32 | intergenic (‑175/+25) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 34.8% | 20.3 / 10.9 | 23 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 812,310 | 0 | C | A | 34.6% | 40.9 / 10.6 | 27 | intergenic (‑59/‑169) | PP_0698/PP_0699 | LysR family transcriptional regulator/LysE family transporter |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 31.4% | 84.3 / 16.6 | 51 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 955,155 | 0 | C | T | 31.0% | 37.8 / 19.0 | 29 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,151 | 0 | G | A | 29.0% | 45.5 / 18.7 | 31 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947_CJ‑RC | 955,152 | 0 | T | A | 29.0% | 40.4 / 22.2 | 31 | intergenic (+106/‑207) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| Marginal new junction evidence (lowest skew 10 of 44 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.110) | 22 (0.350) | 13/222 | 5.5 | 49.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.630) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 39 (0.480) | 16 (0.200) | 14/282 | 6.9 | 30.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 36 (0.460) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 4 (0.050) | 18 (0.220) +GCC |
14/286 | 7.0 | 82.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 4 (0.050) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 652783 | 77 (0.940) | 10 (0.160) | 9/222 | 7.1 | 25.5% | coding (1960/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | 4809912 = | 0 (0.000) | intergenic (‑318/‑237) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 9 (0.110) | 11 (0.160) | 10/240 | 7.2 | 28.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 47 (0.700) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 10 (0.120) | 11 (0.140) | 11/278 | 7.9 | 48.3% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 14 (0.180) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.060) | 11 (0.160) | 9/252 | 8.0 | 30.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 46 (0.650) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4647702 | 18 (0.220) | 5 (0.080) | 4/214 | 9.6 | 31.1% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | = 4647732 | 9 (0.150) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 4 (0.050) | 8 (0.100) +CGGG |
7/284 | 10.0 | 67.3% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 4 (0.050) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 4586141 = | 29 (0.350) | 5 (0.070) | 5/248 | 10.1 | 20.6% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | 4586212 = | 14 (0.200) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||