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 26 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 | 1,070,246 | 1 | . | G | 61.9% | 34.5 / 24.9 | 21 | 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 | 2 | . | A | 61.9% | 31.5 / 25.5 | 21 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,353,311 | 0 | G | C | 58.3% | 3.0 / 13.4 | 12 | T110T (ACG→ACC) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947_CJ‑RC | 4,353,299 | 0 | C | A | 57.1% | 5.9 / 18.0 | 14 | F106L (TTC→TTA) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 51.1% | 22.5 / 192.9 | 134 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.0% | 35.2 / 209.4 | 147 | 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 | 47.5% | 106.4 / 218.3 | 160 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 46.4% | 32.9 / 143.7 | 111 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 45.7% | 34.2 / 13.6 | 35 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 40.5% | 12.5 / 12.1 | 41 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,666,783 | 0 | G | C | 39.3% | 35.7 / 10.4 | 28 | intergenic (‑55/‑216) | PP_1460/ffh | membrane protein/signal recognition particle GTPase subunit |
| * | NC_002947_CJ‑RC | 4,872,423 | 0 | G | T | 34.2% | 74.3 / 11.8 | 39 | intergenic (+70/‑50) | xdhB/xdhC | xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 32.6% | 139.4 / 63.5 | 88 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 32.0% | 31.1 / 14.8 | 26 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 29.2% | 94.7 / 10.5 | 49 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 25.8% | 54.0 / 20.2 | 31 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,356,822 | 0 | T | G | 24.6% | 127.0 / 11.1 | 61 | R28R (CGT→CGG) | PP_3831 | hypothetical protein |
| * | NC_002947_CJ‑RC | 1,497,831 | 0 | T | G | 24.4% | 149.7 / 15.6 | 82 | V140G (GTC→GGC) | PP_1310 | hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 24.1% | 65.9 / 15.0 | 29 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 23.5% | 62.3 / 18.5 | 34 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 19 (0.240) | 23 (0.310) | 17/268 | 5.6 | 55.0% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 20 (0.270) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 42 (0.530) | 19 (0.250) | 18/280 | 5.6 | 32.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 39 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.080) | 17 (0.280) | 12/220 | 5.9 | 46.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 35 (0.580) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 5 (0.060) | 17 (0.220) +GCC |
14/284 | 7.0 | 77.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 5 (0.060) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 15 (0.190) +CGGG |
13/282 | 7.3 | 93.9% | 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 | 3 (0.040) | 13 (0.180) | 12/266 | 7.3 | 46.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 27 (0.370) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 11 (0.160) | 10/250 | 7.6 | 33.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 41 (0.600) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4647702 | 20 (0.250) | 4 (0.070) | 4/212 | 9.7 | 17.9% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | = 4647732 | 22 (0.380) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 24 (0.300) | 11 (0.160) +22 bp |
5/246 | 10.2 | 20.4% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | 4886090 = | 77 (0.970) | intergenic (+53/+76) | PP_4293/yedI | hypothetical protein/inner membrane protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1970739 | 42 (0.530) | 7 (0.100) | 5/250 | 10.3 | 18.6% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947_CJ‑RC | = 1970801 | 25 (0.370) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||