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 | 1,056,264 | 0 | A | C | 68.5% | 143.9 / 82.8 | 91 | L603R (CTG→CGG) | PP_0914 | GGDEF domain‑containing protein |
| * | NC_002947_CJ‑RC | 3,862,282 | 0 | C | G | 66.1% | 76.7 / 72.7 | 63 | A402G (GCC→GGC) | PP_3413 | two‑component system sensor histidine kinase/response regulator |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 55.7% | 15.7 / 114.8 | 97 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 54.4% | ‑1.7 / 120.3 | 91 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,170,180 | 0 | T | G | 53.3% | 0.1 / 13.7 | 15 | intergenic (‑288/‑99) | katG/PP_3669 | catalase‑peroxidase/LysR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.0% | 8.0 / 177.1 | 132 | 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 | 52.8% | 41.1 / 203.8 | 142 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 51.2% | ‑0.5 / 29.6 | 47 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,057,120 | 0 | G | . | 48.4% | 115.2 / 122.1 | 64 | coding (952/2082 nt) | PP_0914 | GGDEF domain‑containing protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 38.3% | 61.5 / 46.0 | 47 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,653,618 | 0 | C | A | 38.1% | 16.5 / 10.1 | 21 | intergenic (+57/‑68) | PP_2325/PP_2326 | 2‑dehydropantoate 2‑reductase/universal stress protein |
| * | NC_002947_CJ‑RC | 5,754,548 | 0 | C | A | 35.7% | 34.7 / 14.5 | 33 | intergenic (‑171/‑300) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 35.4% | 25.9 / 12.4 | 49 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,398,300 | 0 | G | A | 34.9% | 68.3 / 53.9 | 63 | A52V (GCC→GTC) | tphA2II | terephthalate 1,2‑dioxygenase subunit alpha |
| * | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 33.3% | 17.5 / 12.5 | 18 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 33.3% | 9.3 / 13.4 | 18 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 4,935,577 | 0 | T | G | 32.1% | 63.5 / 11.0 | 54 | Q192P (CAG→CCG) | flhF | flagellar biosynthesis protein FlhF |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 30.0% | 20.3 / 17.5 | 20 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 284,586 | 0 | T | A | 29.2% | 27.2 / 10.4 | 28 | intergenic (+33/+30) | betT‑II/atsK | choline/carnitine/betaine transporter/alpha‑ketoglutarate‑dependent sulfonate dioxygenase |
| * | NC_002947_CJ‑RC | 4,140,143 | 0 | G | C | 28.6% | 122.0 / 14.7 | 56 | intergenic (+35/‑230) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 4 (0.060) | 20 (0.370) | 13/222 | 4.5 | 48.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.720) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 9 (0.130) | 14 (0.200) | 12/286 | 6.5 | 52.0% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 17 (0.240) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 1 (0.010) | 11 (0.160) +CGGG |
10/284 | 7.2 | 91.9% | 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) | 9 (0.140) | 9/268 | 7.2 | 33.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 33 (0.510) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 12 (0.170) +GCC |
9/286 | 7.7 | 86.0% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 5873076 = | 23 (0.320) | 4 (0.070) | 4/234 | 9.0 | 19.8% | intergenic (+22/+112) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator |
| ? | NC_002947_CJ‑RC | 5873169 = | 14 (0.250) | intergenic (+115/+19) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 5916999 | 26 (0.360) | 4 (0.070) | 4/236 | 9.1 | 20.0% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | = 5917039 | 11 (0.190) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947_CJ‑RC | 2099960 = | 8 (0.110) | 4 (0.070) | 4/246 | 9.4 | 31.1% | intergenic (‑71/‑134) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein |
| ? | NC_002947_CJ‑RC | 2100055 = | 11 (0.180) | intergenic (‑166/‑39) | PP_1875/PP_1876 | two‑component system sensor histidine kinase/response regulator/AAA family ATP/GTP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5762250 | 25 (0.350) | 3 (0.050) | 3/228 | 9.5 | 13.8% | intergenic (+44/+112) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | = 5762278 | 18 (0.320) | intergenic (+72/+84) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||
| * | ? | NC_002947_CJ‑RC | = 1570426 | 18 (0.250) | 3 (0.050) | 3/240 | 9.9 | 22.4% | intergenic (+34/‑154) | pcaF‑I/pcaT | beta‑ketoadipyl‑CoA thiolase/alpha‑ketoglutarate permease |
| ? | NC_002947_CJ‑RC | = 1570452 | 6 (0.100) | intergenic (+60/‑128) | pcaF‑I/pcaT | beta‑ketoadipyl‑CoA thiolase/alpha‑ketoglutarate permease | |||||