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 34 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 | 4,338,608 | 0 | G | T | 60.0% | 10.5 / 23.1 | 22 | intergenic (+121/+21) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 197,246 | 0 | C | T | 55.1% | 23.6 / 227.3 | 168 | Q918* (CAG→TAG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 55.0% | 9.0 / 26.1 | 24 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.8% | 45.6 / 222.9 | 161 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.2% | ‑3.2 / 23.0 | 24 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 48.2% | 41.2 / 203.5 | 137 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,842,816 | 0 | T | C | 47.8% | 3.4 / 15.2 | 24 | S660G (AGC→GGC) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 47.8% | 15.1 / 19.6 | 50 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 40.3% | 92.6 / 148.0 | 129 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,740,948 | 0 | T | A | 38.9% | 8.3 / 11.7 | 19 | intergenic (+78/+675) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 4,740,951 | 0 | C | G | 38.9% | 5.0 / 19.1 | 18 | intergenic (+81/+672) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 36.8% | 4.8 / 18.9 | 19 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 36.2% | 33.7 / 11.4 | 50 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 35.4% | 103.4 / 20.7 | 65 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 35.0% | 11.6 / 12.3 | 21 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 34.0% | 36.6 / 11.7 | 49 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,740,949 | 0 | T | A | 31.6% | 18.2 / 10.6 | 19 | intergenic (+79/+674) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 5,174,935 | 0 | C | A | 31.6% | 64.0 / 11.2 | 38 | intergenic (‑273/+59) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 29.7% | 113.7 / 14.3 | 64 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 29.6% | 38.2 / 16.5 | 27 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 5 (0.060) | 18 (0.230) | 16/270 | 6.3 | 58.4% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 21 (0.270) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.480) | 19 (0.230) | 17/282 | 6.3 | 31.8% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 42 (0.510) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 20 (0.240) +CGGG |
16/284 | 6.6 | 95.4% | 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 | 3 (0.040) | 16 (0.190) +GCC |
14/286 | 7.3 | 84.5% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 12 (0.150) | 11/268 | 8.0 | 28.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 59 (0.750) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 58 (0.680) | 10 (0.120) | 10/276 | 8.6 | 13.7% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 71 (0.880) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.060) | 9 (0.140) | 5/222 | 9.6 | 23.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 54 (0.830) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 8 (0.090) | 9 (0.110) | 8/278 | 9.6 | 50.5% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 10 (0.120) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 5991572 | 68 (0.800) | 6 (0.070) | 6/276 | 10.7 | 8.2% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991794 = | 71 (0.880) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4959275 | 78 (0.910) | 7 (0.090) | 5/262 | 10.9 | 8.2% | intergenic (‑55/+108) | fliH/fliG | flagellar assembly protein FliH/flagellar motor switch protein |
| ? | NC_002947_CJ‑RC | = 4959335 | 87 (1.140) | intergenic (‑115/+48) | fliH/fliG | flagellar assembly protein FliH/flagellar motor switch protein | |||||