| Variant ID: vg0335310143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35310143 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTGAAAATAGACCCAAAATATTCCTTACTTCCCTAAATGTTTGACGCTGTTGACTTTTTAAAGTATGTTTAACCATTTGTCTTATTCAAAAACTTTTGT[G/A]
AAATATGTAAAACTATATGTATATATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATTATTATTTAAATTTTTTTAAATAAGACGA
TCGTCTTATTTAAAAAAATTTAAATAATAATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTATATATACATATAGTTTTACATATTT[C/T]
ACAAAAGTTTTTGAATAAGACAAATGGTTAAACATACTTTAAAAAGTCAACAGCGTCAAACATTTAGGGAAGTAAGGAATATTTTGGGTCTATTTTCAAA
| 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 | 75.70% | 24.20% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 63.30% | 36.60% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Aus | 269 | 60.60% | 39.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.30% | 21.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 41.50% | 58.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 68.70% | 31.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 58.50% | 41.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 25.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335310143 | G -> A | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 166.0bp to feature; MODIFIER | silent_mutation | Average:65.044; most accessible tissue: Minghui63 root, score: 85.968 | N | N | N | N |
| vg0335310143 | G -> A | LOC_Os03g62314.1 | upstream_gene_variant ; 757.0bp to feature; MODIFIER | silent_mutation | Average:65.044; most accessible tissue: Minghui63 root, score: 85.968 | N | N | N | N |
| vg0335310143 | G -> A | LOC_Os03g62340.1 | downstream_gene_variant ; 2308.0bp to feature; MODIFIER | silent_mutation | Average:65.044; most accessible tissue: Minghui63 root, score: 85.968 | N | N | N | N |