| Variant ID: vg0817015603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015603 |
| 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: 286. )
GAGTCCGGGAAGATATCTGTTGCTTCAATTGTCAAGGAATGGGTCATTTCGCCGACAAGTGCCCAAAACCGAGAAACGTAGCTGCCAGCACGTCAGTCCA[C/T]
GCAAACCCCCGCAATCAGAAGCTTGCTCCTCAACGAATTGTCATCCATGCATCCCGAAGCAGTCCGATAGCCCGCGTTGCAACAGCTCCAACTCCAATGA
TCATTGGAGTTGGAGCTGTTGCAACGCGGGCTATCGGACTGCTTCGGGATGCATGGATGACAATTCGTTGAGGAGCAAGCTTCTGATTGCGGGGGTTTGC[G/A]
TGGACTGACGTGCTGGCAGCTACGTTTCTCGGTTTTGGGCACTTGTCGGCGAAATGACCCATTCCTTGACAATTGAAGCAACAGATATCTTCCCGGACTC
| 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 | 23.70% | 1.10% | 26.64% | 48.60% | NA |
| All Indica | 2759 | 10.10% | 0.00% | 30.52% | 59.37% | NA |
| All Japonica | 1512 | 49.70% | 3.20% | 15.08% | 32.01% | NA |
| Aus | 269 | 17.10% | 0.00% | 39.78% | 43.12% | NA |
| Indica I | 595 | 5.70% | 0.20% | 13.78% | 80.34% | NA |
| Indica II | 465 | 1.90% | 0.00% | 26.45% | 71.61% | NA |
| Indica III | 913 | 17.90% | 0.00% | 44.36% | 37.79% | NA |
| Indica Intermediate | 786 | 9.20% | 0.00% | 29.52% | 61.32% | NA |
| Temperate Japonica | 767 | 72.40% | 0.50% | 8.87% | 18.25% | NA |
| Tropical Japonica | 504 | 20.60% | 7.30% | 18.85% | 53.17% | NA |
| Japonica Intermediate | 241 | 38.20% | 3.30% | 26.97% | 31.54% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 62.50% | 20.83% | NA |
| Intermediate | 90 | 30.00% | 2.20% | 24.44% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015603 | C -> T | LOC_Os08g27910.1 | synonymous_variant ; p.His337His; LOW | synonymous_codon | Average:6.759; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0817015603 | C -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.759; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |