| Variant ID: vg0817015139 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015139 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 195. )
GAGAAGAAATTCCTTCCGAGGTGCACAACAGTTGACAGAGCATCTTTTAGCTAATGGAGGTAGAGTGTCTGATAGTGAAGATTCAGATCAAGTCTCCTCA[G/A]
ATGATGAAGGTGCGAAGCCTCCCCAAGGTTTTAACCAGAATAAAATAGAACTTAAGGCATGCTCTCGTTGTGGAGAAATCGGTCATGTTGCCAGCTCGTG
CACGAGCTGGCAACATGACCGATTTCTCCACAACGAGAGCATGCCTTAAGTTCTATTTTATTCTGGTTAAAACCTTGGGGAGGCTTCGCACCTTCATCAT[C/T]
TGAGGAGACTTGATCTGAATCTTCACTATCAGACACTCTACCTCCATTAGCTAAAAGATGCTCTGTCAACTGTTGTGCACCTCGGAAGGAATTTCTTCTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.20% | 0.40% | 9.52% | 46.87% | NA |
| All Indica | 2759 | 31.80% | 0.00% | 11.85% | 56.36% | NA |
| All Japonica | 1512 | 64.20% | 1.20% | 2.31% | 32.34% | NA |
| Aus | 269 | 26.80% | 0.00% | 31.23% | 42.01% | NA |
| Indica I | 595 | 9.60% | 0.00% | 11.93% | 78.49% | NA |
| Indica II | 465 | 23.00% | 0.00% | 9.89% | 67.10% | NA |
| Indica III | 913 | 53.60% | 0.00% | 11.72% | 34.72% | NA |
| Indica Intermediate | 786 | 28.50% | 0.00% | 13.10% | 58.40% | NA |
| Temperate Japonica | 767 | 81.20% | 0.00% | 0.39% | 18.38% | NA |
| Tropical Japonica | 504 | 36.70% | 3.60% | 5.75% | 53.97% | NA |
| Japonica Intermediate | 241 | 67.20% | 0.00% | 1.24% | 31.54% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 4.44% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015139 | G -> A | LOC_Os08g27910.1 | missense_variant ; p.Asp183Asn; MODERATE | nonsynonymous_codon ; D183N | Average:6.832; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0817015139 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.832; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |