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 | 4,348,812 | 0 | A | G | 62.7% | 54.5 / 118.8 | 118 | 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 | 58.2% | ‑6.6 / 192.1 | 153 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑5.7 / 15.4 | 10 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 49.0% | 43.7 / 142.3 | 102 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 45.6% | 41.4 / 168.8 | 125 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 41.0% | 24.9 / 15.3 | 41 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 34.8% | 26.7 / 16.9 | 23 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 33.3% | 28.8 / 12.0 | 41 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 30.7% | 170.6 / 69.4 | 90 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 3,171,777 | 0 | G | T | 28.0% | 31.9 / 11.0 | 25 | G17C (GGC→TGC) | PP_2784 | short‑chain dehydrogenase/reductase family oxidoreductase |
| * | NC_002947_CJ‑RC | 196,327 | 0 | A | C | 27.3% | 215.6 / 126.2 | 128 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 26.5% | 242.7 / 119.5 | 132 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,306 | 0 | T | C | 25.0% | 210.6 / 83.1 | 125 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 25.0% | 29.9 / 13.3 | 20 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 6,016,653 | 0 | A | G | 24.1% | 50.1 / 14.3 | 29 | intergenic (+43/+67) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| * | NC_002947_CJ‑RC | 6,016,661 | 0 | T | G | 24.1% | 62.2 / 19.1 | 29 | intergenic (+51/+59) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| * | NC_002947_CJ‑RC | 6,016,662 | 0 | C | T | 24.1% | 55.2 / 12.3 | 29 | intergenic (+52/+58) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| * | NC_002947_CJ‑RC | 6,016,660 | 0 | G | C | 23.3% | 72.0 / 18.7 | 30 | intergenic (+50/+60) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 23.3% | 216.4 / 70.1 | 116 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 6,016,667 | 0 | A | G | 22.6% | 60.1 / 13.3 | 32 | intergenic (+57/+53) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 26 (0.350) +GCC |
25/270 | 3.3 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.070) | 18 (0.260) | 18/252 | 4.4 | 30.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 77 (1.100) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 4 (0.050) | 16 (0.220) +CGGG |
13/268 | 6.2 | 80.5% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 4 (0.050) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 5 (0.070) | 11 (0.170) | 10/236 | 6.4 | 25.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 60 (0.920) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1967177 | 32 (0.420) | 7 (0.120) | 5/210 | 8.0 | 22.5% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947_CJ‑RC | = 1967207 | 24 (0.410) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | 1970720 = | 48 (0.630) | 6 (0.090) | 6/236 | 8.2 | 13.2% | intergenic (+14/‑252) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947_CJ‑RC | 1970822 = | 38 (0.580) | intergenic (+116/‑150) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947_CJ‑RC | 1487006 = | 40 (0.520) | 4 (0.070) | 4/216 | 8.8 | 15.9% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | 1487096 = | 11 (0.180) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947_CJ‑RC | 363527 = | 53 (0.690) | 6 (0.090) | 5/242 | 8.9 | 11.8% | intergenic (‑45/+122) | lcdH/PP_0303 | L‑carnitine dehydrogenase/dehydrocarnitine cleavage enzyme |
| ? | NC_002947_CJ‑RC | 363620 = | 43 (0.640) | intergenic (‑138/+29) | lcdH/PP_0303 | L‑carnitine dehydrogenase/dehydrocarnitine cleavage enzyme | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 32 (0.420) | 6 (0.080) | 6/266 | 9.0 | 14.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 41 (0.560) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1114870 = | 27 (0.350) | 4 (0.060) | 4/226 | 9.1 | 13.8% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947_CJ‑RC | 1114946 = | 28 (0.450) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||