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 29 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 | 63.0% | 29.8 / 149.9 | 146 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 57.9% | ‑1.8 / 14.9 | 23 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 55.0% | ‑2.4 / 12.8 | 21 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 54.2% | ‑3.0 / 22.6 | 27 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 50.0% | 11.5 / 10.5 | 25 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 49.0% | 12.0 / 20.9 | 53 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 48.4% | 46.3 / 183.7 | 126 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 44.0% | 9.9 / 10.0 | 25 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 39.5% | 91.1 / 130.9 | 119 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 38.0% | 22.5 / 11.4 | 51 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 34.6% | 34.8 / 13.5 | 52 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,544,489 | 0 | C | A | 32.0% | 39.0 / 22.0 | 25 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,492 | 0 | G | C | 32.0% | 36.4 / 24.4 | 25 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,494 | 0 | C | G | 32.0% | 32.5 / 23.8 | 25 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,499 | 0 | C | G | 32.0% | 38.8 / 21.7 | 25 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,501 | 0 | G | C | 32.0% | 36.6 / 23.1 | 25 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 5,512,699 | 0 | A | C | 29.6% | 108.6 / 10.9 | 56 | K28T (AAG→ACG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 28.6% | 47.0 / 23.1 | 28 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 28.3% | 147.8 / 67.5 | 92 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 27.4% | 124.0 / 22.1 | 78 | T140A (ACC→GCC) | PP_1551 | replication protein O |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 73 (0.870) | 24 (0.330) | 22/252 | 4.1 | 43.3% | 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) | 26 (0.340) | 23/268 | 4.3 | 46.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 56 (0.720) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 23 (0.280) +GCC |
21/286 | 5.2 | 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 | 3 (0.040) | 17 (0.230) | 16/252 | 5.7 | 37.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 55 (0.760) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.070) | 15 (0.230) | 11/222 | 6.6 | 38.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 44 (0.690) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 15 (0.180) | 17 (0.220) | 12/270 | 7.7 | 45.4% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 27 (0.350) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 48 (0.570) | 11 (0.140) | 11/282 | 8.5 | 18.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 52 (0.640) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 60 (0.710) | 10 (0.130) | 10/276 | 8.8 | 15.0% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 57 (0.720) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.020) | 10 (0.120) +CGGG |
8/284 | 10.0 | 83.7% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 1731163 = | 22 (0.260) | 6 (0.090) | 5/236 | 10.2 | 22.3% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947_CJ‑RC | 1731255 = | 24 (0.350) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||