| Variant ID: vg0101920354 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920354 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 390. )
CGTGTAACCACGTGCCACATACCACCACGGTATACAGACGGAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCC[A/G]
CCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCCATGACATCTCGACTACCGGGCCGCAGCTCG
CGAGCTGCGGCCCGGTAGTCGAGATGTCATGGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGG[T/C]
GGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTCCGTCTGTATACCGTGGTGGTATGTGGCACGTGGTTACACG
| 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 | 86.40% | 0.30% | 3.26% | 10.03% | NA |
| All Indica | 2759 | 88.40% | 0.40% | 4.28% | 6.92% | NA |
| All Japonica | 1512 | 79.70% | 0.00% | 2.12% | 18.19% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.00% | 0.37% | NA |
| Indica I | 595 | 76.80% | 0.20% | 8.24% | 14.79% | NA |
| Indica II | 465 | 89.20% | 0.60% | 3.44% | 6.67% | NA |
| Indica III | 913 | 95.00% | 0.10% | 2.41% | 2.52% | NA |
| Indica Intermediate | 786 | 89.10% | 0.80% | 3.94% | 6.23% | NA |
| Temperate Japonica | 767 | 88.70% | 0.00% | 0.39% | 10.95% | NA |
| Tropical Japonica | 504 | 73.20% | 0.00% | 5.36% | 21.43% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 0.83% | 34.44% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 3.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920354 | A -> G | LOC_Os01g04310.1 | synonymous_variant ; p.Gly26Gly; LOW | synonymous_codon | Average:7.78; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |
| vg0101920354 | A -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:7.78; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |