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Detailed information for vg0208665452:
| Variant ID: vg0208665452 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8665452 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )
Flanking Sequence (100 bp) in Reference Genome:
CGATGTGTATCTACAACCTCCCCCCTGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATC[G/T]
ACGTGTACCTAAGACCACTGGTTGAAGATCTTAAACAGTTGTGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAGGACAAACAGGAGGAGTTTAACCTACG
Reverse complement sequence
CGTAGGTTAAACTCCTCCTGTTTGTCCTCGTCCCACACGGGGACACCTTCCTTCTTCCACAACTGTTTAAGATCTTCAACCAGTGGTCTTAGGTACACGT[C/A]
GATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCAGGGGGGAGGTTGTAGATACACATCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.30% | 0.10% | 16.86% | 62.74% | NA |
| All Indica | 2759 | 9.50% | 0.10% | 21.86% | 68.54% | NA |
| All Japonica | 1512 | 44.00% | 0.20% | 9.26% | 46.49% | NA |
| Aus | 269 | 3.00% | 0.00% | 10.04% | 86.99% | NA |
| Indica I | 595 | 16.10% | 0.00% | 24.87% | 58.99% | NA |
| Indica II | 465 | 10.30% | 0.40% | 24.52% | 64.73% | NA |
| Indica III | 913 | 5.00% | 0.00% | 16.98% | 77.98% | NA |
| Indica Intermediate | 786 | 9.30% | 0.00% | 23.66% | 67.05% | NA |
| Temperate Japonica | 767 | 74.60% | 0.00% | 4.17% | 21.25% | NA |
| Tropical Japonica | 504 | 4.40% | 0.60% | 18.85% | 76.19% | NA |
| Japonica Intermediate | 241 | 29.90% | 0.00% | 5.39% | 64.73% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 25.56% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208665452 | G -> T | LOC_Os02g15470.1 | missense_variant ; p.Asp257Tyr; MODERATE | nonsynonymous_codon ; D257Y | Average:14.491; most accessible tissue: Minghui63 root, score: 21.615 | probably damaging  |
3.067 |
DELETERIOUS | 0.00 |
| vg0208665452 | G -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:14.491; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |