| Variant ID: vg0318603436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18603436 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 363. )
GAAAAGGTGGCAGCAATCAAACCTGGAAATAGCGACCCCGCTCTTTTGCACTCTCAACAAGGTTGTTCCAGTGTTTATCTTCCTTCAATGTTGAAGCAGA[A/G]
CCTACAACCTGTGGTATGACAAGTATTATTTGGATTGATAACTAAACCAACAAAGTTAACTACATAAGCAAATAGTGATATAGCCAGAAACAACTGATTG
CAATCAGTTGTTTCTGGCTATATCACTATTTGCTTATGTAGTTAACTTTGTTGGTTTAGTTATCAATCCAAATAATACTTGTCATACCACAGGTTGTAGG[T/C]
TCTGCTTCAACATTGAAGGAAGATAAACACTGGAACAACCTTGTTGAGAGTGCAAAAGAGCGGGGTCGCTATTTCCAGGTTTGATTGCTGCCACCTTTTC
| 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 | 97.10% | 0.10% | 0.47% | 2.31% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 91.30% | 0.20% | 1.32% | 7.14% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 77.60% | 0.60% | 3.37% | 18.45% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 1.24% | 6.22% | NA |
| VI/Aromatic | 96 | 95.80% | 3.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318603436 | A -> DEL | LOC_Os03g32526.1 | N | frameshift_variant | Average:7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0318603436 | A -> G | LOC_Os03g32526.1 | synonymous_variant ; p.Gly731Gly; LOW | synonymous_codon | Average:7.885; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |