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 25 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 | 5,684,230 | 4 | . | G | 100.0% | 10.4 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 57.7% | 36.2 / 37.1 | 27 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 57.1% | ‑6.5 / 11.2 | 16 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 55.6% | 33.0 / 41.9 | 27 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.6% | 26.8 / 153.8 | 110 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 48.2% | 39.0 / 161.0 | 111 | 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 | 44.8% | 8.9 / 12.8 | 31 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,174,938 | 0 | G | C | 43.8% | 32.4 / 14.2 | 32 | intergenic (‑276/+56) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 42.9% | 24.8 / 13.8 | 43 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 40.5% | 69.7 / 132.6 | 116 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 34.2% | 21.1 / 11.1 | 39 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 3,989,361 | 0 | A | C | 32.2% | 102.9 / 16.4 | 59 | T627P (ACC→CCC) | oplA | 5‑oxoprolinase A |
| * | NC_002947_CJ‑RC | 4,044,569 | 0 | A | C | 31.5% | 88.3 / 11.1 | 54 | V380G (GTG→GGG) | PP_3566 | MFS transporter |
| * | NC_002947_CJ‑RC | 5,694,794 | 0 | A | C | 30.0% | 132.0 / 16.8 | 80 | P118P (CCA→CCC) | PP_4994 | hypothetical protein |
| * | NC_002947_CJ‑RC | 1,544,359 | 0 | C | G | 28.6% | 47.2 / 12.3 | 28 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 4,942,564 | 0 | G | T | 28.4% | 195.5 / 13.7 | 81 | V105L (GTA→TTA) | PP_4348 | cystathionine beta‑lyase |
| * | NC_002947_CJ‑RC | 1,404,025 | 0 | A | C | 27.6% | 122.5 / 12.3 | 58 | F553V (TTC→GTC) | PP_1228 | methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 3,660,700 | 0 | C | G | 25.4% | 137.8 / 13.3 | 63 | C12S (TGC→TCC) | PP_3224 | class II aldolase/adducin domain‑containing protein |
| * | NC_002947_CJ‑RC | 4,433,580 | 0 | G | C | 25.0% | 111.5 / 10.1 | 56 | intergenic (‑29/‑89) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 251,249 | 0 | A | C | 24.1% | 119.8 / 12.3 | 58 | intergenic (‑47/‑19) | nfeD/PP_0201 | membrane bound peptidase NefD/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 22 (0.420) | 15/222 | 3.6 | 64.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 20 (0.380) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 63 (0.910) | 20 (0.300) | 18/276 | 4.0 | 29.7% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 35 (0.530) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 16 (0.230) +GCC |
14/286 | 5.3 | 89.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 34 (0.490) | 11 (0.160) | 11/282 | 6.2 | 25.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 32 (0.480) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.060) | 13 (0.200) | 10/268 | 6.3 | 29.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 59 (0.920) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.060) | 6 (0.100) | 5/252 | 8.3 | 25.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 32 (0.530) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 76 (1.090) | 5 (0.080) | 5/258 | 8.4 | 7.6% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 55 (0.890) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 49 (0.700) | 4 (0.080) | 3/222 | 8.7 | 9.5% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 39 (0.740) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 22 (0.320) | 5 (0.080) | 5/274 | 8.8 | 13.1% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 46 (0.700) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 5 (0.070) +CGGG |
5/284 | 9.1 | 83.7% | 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 | |||||