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Detailed information for vg0512045644:
| Variant ID: vg0512045644 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045644 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 218. )
Flanking Sequence (100 bp) in Reference Genome:
AATTCCTTCAGTCTCAAGGTAACTGCCACGGTCACTTCCCTGGGGTTGGCGAGGATGGTAGCGATACTCAGTGTCGGCCAATTGATCACTGTAGCGATCA[C/T]
GGAGCTCTCCTATGGCGATCCTTGCCACCTCCTGACATGCATGGATGTAGTTTCTTCCTCCAGCTTCAAACATCACTGAGGGGATATCTTCACTATTACT
Reverse complement sequence
AGTAATAGTGAAGATATCCCCTCAGTGATGTTTGAAGCTGGAGGAAGAAACTACATCCATGCATGTCAGGAGGTGGCAAGGATCGCCATAGGAGAGCTCC[G/A]
TGATCGCTACAGTGATCAATTGGCCGACACTGAGTATCGCTACCATCCTCGCCAACCCCAGGGAAGTGACCGTGGCAGTTACCTTGAGACTGAAGGAATT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.60% | 0.30% | 4.17% | 9.94% | NA |
| All Indica | 2759 | 83.70% | 0.50% | 6.81% | 8.95% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.33% | NA |
| Aus | 269 | 21.20% | 0.00% | 1.49% | 77.32% | NA |
| Indica I | 595 | 90.60% | 0.70% | 4.03% | 4.71% | NA |
| Indica II | 465 | 96.80% | 0.20% | 1.94% | 1.08% | NA |
| Indica III | 913 | 74.00% | 0.70% | 10.95% | 14.35% | NA |
| Indica Intermediate | 786 | 82.10% | 0.40% | 7.00% | 10.56% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 3.33% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045644 | C -> T | LOC_Os05g20520.1 | missense_variant ; p.Arg113His; MODERATE | nonsynonymous_codon ; R113H | Average:7.575; most accessible tissue: Zhenshan97 flower, score: 17.42 | probably damaging  |
2.33 |
DELETERIOUS | 0.01 |
| vg0512045644 | C -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:7.575; most accessible tissue: Zhenshan97 flower, score: 17.42 | N | N | N | N |