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 22 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 | 1,327,121 | 0 | C | T | 52.7% | 47.5 / 206.9 | 147 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.2% | ‑4.5 / 21.7 | 24 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.9% | ‑6.6 / 146.2 | 107 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.2% | 23.4 / 167.3 | 121 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 50.0% | 2.8 / 10.1 | 24 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 50.0% | 6.1 / 13.7 | 28 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,842,816 | 0 | T | C | 48.3% | 8.2 / 20.1 | 30 | S660G (AGC→GGC) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 45.5% | ‑4.0 / 11.6 | 11 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 42.5% | 11.0 / 14.3 | 42 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 41.7% | 74.6 / 120.3 | 108 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 31.4% | 70.6 / 15.8 | 52 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 117,276 | 0 | C | G | 30.2% | 75.7 / 10.2 | 44 | intergenic (+56/+38) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 30.2% | 115.8 / 10.9 | 53 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 23.9% | 158.2 / 36.1 | 73 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 197,590 | 0 | T | C | 23.9% | 208.8 / 68.8 | 114 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,694,794 | 0 | A | C | 23.5% | 117.2 / 13.3 | 69 | P118P (CCA→CCC) | PP_4994 | hypothetical protein |
| * | NC_002947_CJ‑RC | 2,737,081 | 0 | C | A | 23.1% | 111.7 / 10.7 | 52 | Q1327K (CAA→AAA) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 23.0% | 211.6 / 82.7 | 113 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 22.7% | 217.8 / 81.8 | 110 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 197,572 | 0 | G | A | 21.6% | 244.2 / 57.2 | 116 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 33 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 56 (0.760) | 21 (0.330) | 18/252 | 4.2 | 46.5% | 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 | 4809877 = | 7 (0.100) | 20 (0.360) | 13/222 | 4.9 | 43.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 46 (0.830) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 31 (0.420) | 18 (0.250) | 17/282 | 5.3 | 33.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 41 (0.580) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.080) | 17 (0.250) | 15/268 | 5.5 | 47.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 32 (0.470) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 12 (0.160) | 13 (0.190) | 13/278 | 6.4 | 56.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 9 (0.130) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.080) | 11 (0.170) | 9/252 | 7.3 | 25.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 58 (0.920) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 20 (0.270) | 12 (0.170) | 11/286 | 7.4 | 37.7% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 20 (0.280) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 28 (0.380) | 10 (0.140) | 10/278 | 7.6 | 17.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 68 (0.970) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 13 (0.180) +GCC |
10/286 | 7.8 | 86.9% | 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 | 2954632 = | 37 (0.500) | 5 (0.080) | 5/244 | 9.2 | 13.7% | intergenic (‑135/‑146) | PP_2586/PP_2587 | putative amino acid transporter/LuxR family transcriptional regulator |
| ? | NC_002947_CJ‑RC | 2954698 = | 32 (0.520) | intergenic (‑201/‑80) | PP_2586/PP_2587 | putative amino acid transporter/LuxR family transcriptional regulator | |||||