| Variant ID: vg0138753386 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38753386 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 263. )
ATGAATGAGAACACAAGGCGCATGATAATTTTTCACAAGAAAGGCTTGTGTGCCATTTGTGTGGTTCCGGGAAATATAGTGTGTTTTACTCTTGGTAGTT[C/A]
TAGTGAATTGACAATGGTGTGATGTAACTAGTTTTTGGCTAGGGAAAAGTGAAGTGCTTCTATTTCATAGTTTTCGTACTGAATGGAAAATATTTAGTTA
TAACTAAATATTTTCCATTCAGTACGAAAACTATGAAATAGAAGCACTTCACTTTTCCCTAGCCAAAAACTAGTTACATCACACCATTGTCAATTCACTA[G/T]
AACTACCAAGAGTAAAACACACTATATTTCCCGGAACCACACAAATGGCACACAAGCCTTTCTTGTGAAAAATTATCATGCGCCTTGTGTTCTCATTCAT
| 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 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 74.00% | 26.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0138753386 | C -> A | LOC_Os01g66710.1 | downstream_gene_variant ; 2618.0bp to feature; MODIFIER | silent_mutation | Average:44.016; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0138753386 | C -> A | LOC_Os01g66730.1 | downstream_gene_variant ; 1672.0bp to feature; MODIFIER | silent_mutation | Average:44.016; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0138753386 | C -> A | LOC_Os01g66730.2 | downstream_gene_variant ; 1700.0bp to feature; MODIFIER | silent_mutation | Average:44.016; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0138753386 | C -> A | LOC_Os01g66720.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.016; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |