| Variant ID: vg0510478732 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478732 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 295. )
ACTTGGGTACATTGCTCGGCTCGCCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACTCTGATCAGAGGTGTACAACTTTACCCACAAGACACATC[T/A]
TCCTCACGTGCAACCACGTGCCACATACCACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCC
GGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGTGGTTGCACGTGAGGA[A/T]
GATGTGTCTTGTGGGTAAAGTTGTACACCTCTGATCAGAGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGGCGAGCCGAGCAATGTACCCAAGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.10% | 1.80% | 1.10% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.50% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 55.80% | 26.40% | 17.84% | 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 | 98.80% | 0.90% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.60% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478732 | T -> A | LOC_Os05g18210.1 | downstream_gene_variant ; 1565.0bp to feature; MODIFIER | silent_mutation | Average:23.33; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg0510478732 | T -> A | LOC_Os05g18230.1 | downstream_gene_variant ; 2416.0bp to feature; MODIFIER | silent_mutation | Average:23.33; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
| vg0510478732 | T -> A | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:23.33; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |