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 44 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 | 195,634 | 0 | C | T | 58.7% | 25.2 / 127.9 | 109 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,164,212 | 0 | G | T | 57.1% | 1.8 / 12.2 | 15 | intergenic (+32/+169) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 56.2% | ‑3.1 / 12.4 | 16 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.7% | 0.6 / 139.3 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,164,209 | 0 | C | G | 52.9% | 4.7 / 16.5 | 17 | intergenic (+29/+172) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 45.2% | 43.2 / 184.1 | 136 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 44.4% | ‑1.8 / 10.1 | 9 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 4,032,165 | 0 | C | A | 40.0% | 30.7 / 12.2 | 25 | intergenic (+58/‑198) | PP_3554/PP_3555 | acyl‑CoA dehydrogenase family protein/transmembrane sensor |
| * | NC_002947_CJ‑RC | 1,666,787 | 0 | G | C | 38.7% | 40.3 / 13.9 | 31 | intergenic (‑59/‑212) | PP_1460/ffh | membrane protein/signal recognition particle GTPase subunit |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 38.1% | 29.3 / 12.9 | 46 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 37.9% | 38.7 / 10.8 | 29 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 1,544,489 | 0 | C | A | 37.5% | 10.3 / 15.2 | 16 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 37.5% | 8.1 / 18.3 | 16 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 36.8% | 206.8 / 165.5 | 167 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,112 | 0 | G | C | 36.7% | 28.4 / 12.3 | 30 | intergenic (+39/‑712) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 35.4% | 142.8 / 88.1 | 98 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,544,492 | 0 | G | C | 35.3% | 17.0 / 16.9 | 17 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,494 | 0 | C | G | 35.3% | 15.5 / 16.9 | 17 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,499 | 0 | C | G | 35.3% | 17.0 / 16.9 | 17 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,501 | 0 | G | C | 35.3% | 16.9 / 16.9 | 17 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 54 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 36 (0.470) | 17 (0.230) | 17/280 | 5.4 | 30.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 42 (0.570) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 13 (0.180) +CGGG |
12/282 | 7.1 | 93.0% | 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 | = 5558423 | 1 (0.010) | 11 (0.150) +GCC |
10/284 | 8.0 | 91.8% | 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 | 4809877 = | 5 (0.070) | 9 (0.160) | 6/220 | 8.1 | 27.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 43 (0.740) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 5596907 = | 26 (0.340) | 6 (0.100) | 6/234 | 8.5 | 23.5% | intergenic (‑39/+106) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase |
| ? | NC_002947_CJ‑RC | 5597000 = | 18 (0.290) | intergenic (‑132/+13) | PP_4921/thiC | NCS1 family transporter/phosphomethylpyrimidine synthase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 63 (0.830) | 8 (0.120) | 7/250 | 8.5 | 22.8% | 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 | = 4809882 | 3 (0.040) | 6 (0.090) | 6/266 | 9.5 | 18.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 49 (0.700) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 5 (0.080) | 5/250 | 9.6 | 15.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 54 (0.820) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 5916972 = | 28 (0.370) | 4 (0.070) | 4/234 | 9.8 | 16.5% | 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 | |||||
| * | ? | NC_002947_CJ‑RC | 2472102 = | 38 (0.500) | 3 (0.050) | 3/212 | 9.8 | 11.2% | intergenic (+6/+143) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472226 = | 20 (0.360) | intergenic (+130/+19) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||