| Variant ID: vg0202540495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2540495 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 340. )
ATTTACATCTGCTCGTAGCATCCTGATAATACTAGAAGATCCATGTAGTTCTTTGAGTACCTACTCGATATTCTCTGCTATATATCTTGCCTTCTAGAAA[G/T]
TATTTTTCAGGAACAATTGAGCACTTGAGTAGGATGTGGTCGAGTACACTGCATTATCAAGAACGTTCTTGACAAATGCAGAGTCGTCGCGCCCAACCAA
TTGGTTGGGCGCGACGACTCTGCATTTGTCAAGAACGTTCTTGATAATGCAGTGTACTCGACCACATCCTACTCAAGTGCTCAATTGTTCCTGAAAAATA[C/A]
TTTCTAGAAGGCAAGATATATAGCAGAGAATATCGAGTAGGTACTCAAAGAACTACATGGATCTTCTAGTATTATCAGGATGCTACGAGCAGATGTAAAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540495 | G -> T | LOC_Os02g05270.1 | upstream_gene_variant ; 4320.0bp to feature; MODIFIER | N | Average:53.619; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0202540495 | G -> T | LOC_Os02g05280.1 | downstream_gene_variant ; 1825.0bp to feature; MODIFIER | N | Average:53.619; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0202540495 | G -> T | LOC_Os02g05300.1 | downstream_gene_variant ; 1595.0bp to feature; MODIFIER | N | Average:53.619; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0202540495 | G -> T | LOC_Os02g05290.1 | intron_variant ; MODIFIER | N | Average:53.619; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |