| Variant ID: vg0811599017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599017 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )
CCGGCCTCGTCGTTGCTGTCGTCCGCACCATCGTCACCGCCCTCCTCGTCGGAGTCGAGGGCGAACGCGAGCTGAGGGGCCGTACCCTCGAAGCTGTGGA[C/A]
GATGTGGTCGGCGGCGTCCCGGACCTGCGCGCGCGCGCCGTCCTCGGTTCCGGGAGGGAACTCTTCCAGCGCTGCCCACGGGGAGAAGTCAGGGTCCCTG
CAGGGACCCTGACTTCTCCCCGTGGGCAGCGCTGGAAGAGTTCCCTCCCGGAACCGAGGACGGCGCGCGCGCGCAGGTCCGGGACGCCGCCGACCACATC[G/T]
TCCACAGCTTCGAGGGTACGGCCCCTCAGCTCGCGTTCGCCCTCGACTCCGACGAGGAGGGCGGTGACGATGGTGCGGACGACAGCAACGACGAGGCCGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.90% | 3.50% | 8.70% | 66.86% | NA |
| All Indica | 2759 | 3.20% | 5.70% | 9.13% | 81.99% | NA |
| All Japonica | 1512 | 52.50% | 0.30% | 4.96% | 42.20% | NA |
| Aus | 269 | 28.60% | 0.40% | 25.65% | 45.35% | NA |
| Indica I | 595 | 0.70% | 2.90% | 3.70% | 92.77% | NA |
| Indica II | 465 | 0.60% | 2.60% | 3.44% | 93.33% | NA |
| Indica III | 913 | 5.50% | 11.30% | 13.69% | 69.55% | NA |
| Indica Intermediate | 786 | 3.80% | 3.30% | 11.32% | 81.55% | NA |
| Temperate Japonica | 767 | 82.00% | 0.10% | 2.35% | 15.51% | NA |
| Tropical Japonica | 504 | 18.10% | 0.80% | 9.13% | 72.02% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.00% | 4.56% | 64.73% | NA |
| VI/Aromatic | 96 | 11.50% | 2.10% | 7.29% | 79.17% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 8.89% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599017 | C -> A | LOC_Os08g19400.1 | missense_variant ; p.Val296Phe; MODERATE | nonsynonymous_codon ; V296F | Average:18.99; most accessible tissue: Zhenshan97 flower, score: 29.832 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811599017 | C -> DEL | LOC_Os08g19400.1 | N | frameshift_variant | Average:18.99; most accessible tissue: Zhenshan97 flower, score: 29.832 | N | N | N | N |