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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 76.0% | 56.1 / 16.6 | 25 | 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 | 1 | . | G | 72.7% | 47.3 / 16.3 | 25 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 63.2% | 106.3 / 143.1 | 144 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 57.6% | 9.2 / 124.2 | 107 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.4% | 39.4 / 239.8 | 174 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 50.0% | ‑6.4 / 13.1 | 16 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,840,084 | 0 | T | G | 42.4% | 40.2 / 10.5 | 33 | intergenic (+16/+20) | PP_1646/PP_1647 | thioredoxin/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 38.0% | 27.9 / 14.8 | 58 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 3,312,690 | 0 | A | T | 30.8% | 50.7 / 13.7 | 44 | intergenic (+31/‑131) | PP_2912/hemB | hypothetical protein/5‑aminolevulinate dehydratase |
| * | NC_002947_CJ‑RC | 3,773,220 | 0 | T | G | 28.4% | 137.8 / 11.2 | 67 | intergenic (+34/‑78) | PP_3333/PP_5743 | hypothetical protein/TonB‑dependent receptor protein |
| * | NC_002947_CJ‑RC | 3,478,006 | 0 | A | C | 28.0% | 82.3 / 10.3 | 51 | intergenic (‑41/+55) | PP_3088/PP_3089 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,285,059 | 0 | T | G | 25.9% | 117.3 / 11.4 | 54 | L97R (CTG→CGG) | PP_1122 | OmpA family protein |
| * | NC_002947_CJ‑RC | 4,122,032 | 0 | C | A | 25.4% | 165.9 / 16.1 | 64 | G202C (GGC→TGC) | PP_3625 | LysE family transporter |
| * | NC_002947_CJ‑RC | 6,000,004 | 1 | . | G | 23.8% | 40.0 / 19.8 | 21 | intergenic (‑158/+42) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 3,653,469 | 0 | G | C | 22.6% | 168.7 / 10.9 | 62 | intergenic (+35/+63) | PP_3218/PP_3219 | NtaA/SnaA/SoxA family monooxygenase/alkansulfonate monooxygenase |
| * | NC_002947_CJ‑RC | 4,960 | 0 | C | A | 22.1% | 171.0 / 10.4 | 68 | intergenic (‑579/+52) | trmF/trmE | tRNA uridine 5‑carboxymethylaminomethyl modification protein/GTPase |
| * | NC_002947_CJ‑RC | 6,000,009 | 0 | C | . | 21.7% | 53.6 / 13.1 | 23 | intergenic (‑163/+37) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 248,861 | 0 | C | A | 20.2% | 242.8 / 13.2 | 84 | Q148K (CAA→AAA) | PP_0198 | putative transporter |
| Marginal new junction evidence (lowest skew 10 of 34 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 14 (0.240) | 11/222 | 5.5 | 36.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 45 (0.770) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 353066 | 9 (0.120) | 16 (0.220) | 13/280 | 6.4 | 57.5% | intergenic (+33/+85) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| ? | NC_002947_CJ‑RC | = 6011988 | 15 (0.200) | intergenic (+70/+12) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 13 (0.170) +GCC |
13/286 | 6.6 | 81.6% | 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 | = 1780066 | 15 (0.200) | 10 (0.140) | 10/278 | 7.5 | 46.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 9 (0.120) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 10 (0.130) +CGGG |
9/284 | 8.1 | 91.1% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.030) | 8 (0.110) | 7/268 | 8.7 | 19.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 65 (0.930) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 337781 = | 13 (0.170) | 5 (0.080) | 5/236 | 8.9 | 24.7% | intergenic (‑31/+98) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947_CJ‑RC | 337865 = | 20 (0.320) | intergenic (‑115/+14) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||
| * | ? | NC_002947_CJ‑RC | 5391028 = | 51 (0.670) | 4 (0.060) | 4/238 | 9.6 | 8.7% | intergenic (+24/‑296) | dld2/PP_4738 | D‑lactate dehydrogenase/hypothetical protein |
| ? | NC_002947_CJ‑RC | 5391137 = | 42 (0.670) | intergenic (+133/‑187) | dld2/PP_4738 | D‑lactate dehydrogenase/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652783 | 68 (0.890) | 3 (0.050) | 3/222 | 9.8 | 10.4% | 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 | 5916972 = | 32 (0.420) | 4 (0.060) | 3/236 | 10.3 | 15.4% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | 5917068 = | 18 (0.290) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||