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 33 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 | 5,684,230 | 4 | . | G | 100.0% | 10.5 / NA | 5 | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 69.2% | 39.5 / 25.2 | 26 | 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 | 69.2% | 44.2 / 24.6 | 26 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,843,091 | 0 | A | C | 63.0% | 34.8 / 21.7 | 27 | V568G (GTG→GGG) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 50.0% | 25.6 / 144.4 | 103 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 49.4% | 22.5 / 119.6 | 81 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 49.1% | 13.9 / 158.1 | 108 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 44.9% | 71.6 / 113.1 | 90 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 35.4% | 96.1 / 78.0 | 79 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,754,548 | 0 | C | A | 35.0% | 18.7 / 10.8 | 24 | intergenic (‑171/‑300) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 1,752,323 | 0 | A | C | 34.5% | 82.9 / 17.4 | 58 | K8T (AAG→ACG) | PP_1553 | hypothetical protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 29.8% | 167.1 / 58.4 | 85 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,403,591 | 0 | T | C | 29.2% | 19.5 / 14.5 | 27 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 28.0% | 210.3 / 88.9 | 108 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,403,590 | 0 | G | A | 28.0% | 32.0 / 12.7 | 27 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 27.6% | 72.2 / 26.3 | 29 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 197,590 | 0 | T | C | 27.2% | 143.5 / 64.4 | 92 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 26.7% | 74.8 / 11.6 | 48 | T140A (ACC→GCC) | PP_1551 | replication protein O |
| * | NC_002947_CJ‑RC | 790,253 | 0 | A | C | 26.4% | 104.1 / 10.2 | 53 | A139A (GCT→GCG) | PP_0676 | transcription elongation factor |
| * | NC_002947_CJ‑RC | 197,572 | 0 | G | A | 25.8% | 164.6 / 59.9 | 93 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 12 (0.210) +GCC |
10/284 | 5.5 | 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 | = 652782 | 46 (0.780) | 9 (0.180) | 8/250 | 5.6 | 31.2% | 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 | 1737987 = | 65 (1.100) | 8 (0.150) | 7/256 | 6.1 | 12.9% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 51 (0.970) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 7 (0.140) | 6/250 | 6.5 | 21.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 52 (1.020) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 29 (0.490) | 7 (0.120) | 7/280 | 6.6 | 16.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 43 (0.750) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 10 (0.170) | 6 (0.110) | 6/276 | 7.0 | 27.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 23 (0.410) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 3968879 | NA (NA) | 5 (0.090) | 5/276 | 7.6 | 10.4% | coding (1007/1179 nt) | PP_3498 | transposase |
| ? | NC_002947_CJ‑RC | 3968942 = | 45 (0.760) | coding (1070/1179 nt) | PP_3498 | transposase | |||||
| * | ? | NC_002947_CJ‑RC | 2429885 = | 18 (0.300) | 3 (0.070) | 3/224 | 7.6 | 18.8% | intergenic (+15/+98) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase |
| ? | NC_002947_CJ‑RC | 2429966 = | 12 (0.260) | intergenic (+96/+17) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.020) | 6 (0.100) +CGGG |
5/282 | 7.7 | 86.1% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.020) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 337790 | 7 (0.120) | 4 (0.070) | 4/278 | 8.2 | 26.1% | intergenic (‑40/+89) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947_CJ‑RC | 337853 = | 16 (0.280) | intergenic (‑103/+26) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||