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 30 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 | 278,742 | 1 | . | A | 74.2% | 72.9 / 23.8 | 31 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| * | NC_002947_CJ‑RC | 4,032,154 | 0 | G | T | 54.2% | 18.5 / 35.2 | 24 | intergenic (+47/‑209) | PP_3554/PP_3555 | acyl‑CoA dehydrogenase family protein/transmembrane sensor |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.5% | ‑1.1 / 132.3 | 97 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.4% | 20.0 / 194.0 | 140 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 50.0% | 1.0 / 17.4 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 50.0% | ‑0.5 / 11.8 | 30 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.2% | 65.9 / 189.4 | 134 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 42.4% | 87.6 / 144.9 | 130 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 42.3% | 22.2 / 10.7 | 26 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 3,466,841 | 0 | T | G | 39.3% | 13.3 / 13.0 | 30 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 856,594 | 0 | G | T | 38.2% | 34.2 / 10.1 | 35 | intergenic (+24/+92) | pagL‑I/PP_0738 | lipid A 3‑O‑deacylase/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 34.8% | 20.7 / 15.8 | 24 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 33.3% | 115.5 / 81.6 | 95 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 30.5% | 179.8 / 111.9 | 118 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 30.0% | 187.8 / 114.4 | 120 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 28.2% | 168.8 / 86.8 | 117 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,531,676 | 0 | T | G | 27.9% | 98.1 / 14.5 | 61 | Q67P (CAG→CCG) | PP_1344 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 26.9% | 116.5 / 10.3 | 68 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 5,392,142 | 0 | C | G | 26.2% | 119.2 / 25.9 | 65 | intergenic (+528/‑194) | PP_4738/PP_mr56 | hypothetical protein/C4 ncRNA |
| * | NC_002947_CJ‑RC | 117,248 | 0 | C | A | 25.4% | 99.1 / 10.5 | 55 | intergenic (+28/+66) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.560) | 21 (0.300) | 20/284 | 4.6 | 35.1% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 38 (0.530) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 56 (0.760) | 17 (0.240) | 16/278 | 5.6 | 25.6% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 46 (0.660) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 18 (0.240) | 16 (0.230) | 14/280 | 6.3 | 53.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 11 (0.160) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 19 (0.280) | 12/270 | 6.8 | 40.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 53 (0.780) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 23 (0.310) | 11 (0.160) | 11/280 | 7.5 | 21.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 59 (0.840) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 4 (0.050) | 13 (0.180) +GCC |
11/288 | 7.7 | 76.8% | 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 | 1737987 = | 65 (0.880) | 7 (0.110) | 7/260 | 8.8 | 9.3% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 79 (1.220) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2282748 | 14 (0.190) | 7 (0.100) | 7/282 | 9.5 | 30.8% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 18 (0.260) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809876 = | 9 (0.120) | 10 (0.140) | 5/290 | 10.9 | 34.6% | intergenic (‑282/‑273) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 4947075 | 29 (0.400) | intergenic (+732/+66) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4872393 | 23 (0.310) | 3 (0.050) | 3/244 | 11.0 | 15.8% | intergenic (+40/‑80) | xdhB/xdhC | xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor |
| ? | NC_002947_CJ‑RC | = 4872413 | 13 (0.210) | intergenic (+60/‑60) | xdhB/xdhC | xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor | |||||