| Variant ID: vg0108239058 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8239058 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
GTCCACGCCTGCACGGCTGGCCTATTATGCCGCCGCTGTTGGGCGCCTACGTCTTCACCGACCGGCTCGCCTTCGCCGCCGCCGACTGGTGTCCTCGCCT[G/A]
CACGGCTGGCCTATTATGCCGCCGTTGTTGGGCGCCTACGTCTTCACCGACCGGCTTGCCTTCGCCGCCGCCAACTGGTGTTTCCGCCTGCACGGCTAGC
GCTAGCCGTGCAGGCGGAAACACCAGTTGGCGGCGGCGAAGGCAAGCCGGTCGGTGAAGACGTAGGCGCCCAACAACGGCGGCATAATAGGCCAGCCGTG[C/T]
AGGCGAGGACACCAGTCGGCGGCGGCGAAGGCGAGCCGGTCGGTGAAGACGTAGGCGCCCAACAGCGGCGGCATAATAGGCCAGCCGTGCAGGCGTGGAC
| 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 | 98.00% | 0.20% | 0.95% | 0.87% | NA |
| All Indica | 2759 | 97.90% | 0.30% | 0.54% | 1.23% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.13% | 0.20% | NA |
| Aus | 269 | 89.60% | 0.00% | 10.41% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.00% | 0.17% | 0.50% | NA |
| Indica II | 465 | 93.50% | 0.00% | 1.29% | 5.16% | NA |
| Indica III | 913 | 99.00% | 0.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 0.00% | 0.89% | 0.89% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108239058 | G -> A | LOC_Os01g14720.1 | upstream_gene_variant ; 3225.0bp to feature; MODIFIER | silent_mutation | Average:47.46; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0108239058 | G -> A | LOC_Os01g14750.1 | downstream_gene_variant ; 3568.0bp to feature; MODIFIER | silent_mutation | Average:47.46; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0108239058 | G -> A | LOC_Os01g14730.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.46; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
| vg0108239058 | G -> DEL | N | N | silent_mutation | Average:47.46; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |