| Variant ID: vg0221476579 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21476579 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.25, others allele: 0.00, population size: 218. )
GGCCAGCATGCGGTTGCCGTCTTCCAAGCAGTAGCCCAAGAGCTCCAGGAAGTACTCGTTCTTGAGCTTGGACACCATCGCTATCTATGGCGACGAGATG[A/G]
AGATGAGCAAAAAGCTAAGATGGCTCATGTCGCGAGGAGGAGGAAGAAGAAGAAGTGGGGTGTTTTGGGGCACACCTGGGCGGAGAACTCGGAGTCGGTC
GACCGACTCCGAGTTCTCCGCCCAGGTGTGCCCCAAAACACCCCACTTCTTCTTCTTCCTCCTCCTCGCGACATGAGCCATCTTAGCTTTTTGCTCATCT[T/C]
CATCTCGTCGCCATAGATAGCGATGGTGTCCAAGCTCAAGAACGAGTACTTCCTGGAGCTCTTGGGCTACTGCTTGGAAGACGGCAACCGCATGCTGGCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 4.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 63.20% | 36.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.10% | 6.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221476579 | A -> G | LOC_Os02g35750.1 | downstream_gene_variant ; 2757.0bp to feature; MODIFIER | silent_mutation | Average:70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221476579 | A -> G | LOC_Os02g35750.2 | downstream_gene_variant ; 1111.0bp to feature; MODIFIER | silent_mutation | Average:70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221476579 | A -> G | LOC_Os02g35750.3 | downstream_gene_variant ; 946.0bp to feature; MODIFIER | silent_mutation | Average:70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221476579 | A -> G | LOC_Os02g35760.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221476579 | A -> G | LOC_Os02g35760.2 | intron_variant ; MODIFIER | silent_mutation | Average:70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |