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Detailed information for vg0216160760:
| Variant ID: vg0216160760 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 16160760 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
CTCAACACCACAACACACCAAATTCAATCAACTATTGCTCACCTCGTGGTCAGGGCAAGTGTAGAAAATGCGATCTGGATTACTAGCTGTCTTCGATGTG[C/T]
GCTTCACGACGGTTTTATTCTCGCACGATGGGCACAGGATCAATGGTACCTTCTTCCGGCGAGTACAAGCGGAGGCCGGGCTTGAAGAAGCCATGGGGGC
Reverse complement sequence
GCCCCCATGGCTTCTTCAAGCCCGGCCTCCGCTTGTACTCGCCGGAAGAAGGTACCATTGATCCTGTGCCCATCGTGCGAGAATAAAACCGTCGTGAAGC[G/A]
CACATCGAAGACAGCTAGTAATCCAGATCGCATTTTCTACACTTGCCCTGACCACGAGGTGAGCAATAGTTGATTGAATTTGGTGTGTTGTGGTGTTGAG
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 | 94.90% | 4.80% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 94.90% | 4.60% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 87.50% | 9.70% | 2.80% | 0.00% | NA |
| Indica III | 913 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0216160760 | C -> T | LOC_Os02g27430.1 | missense_variant ; p.Arg44His; MODERATE | nonsynonymous_codon ; R44H | Average:57.837; most accessible tissue: Zhenshan97 young leaf, score: 82.982 | probably damaging  |
2.48 |
DELETERIOUS | 0.04 |