| Variant ID: vg0139403433 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39403433 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )
GAAGCCCTTTTGTGAACACATCCGCGAACTGATGGGCACTCGGTATCGGTAGGACGCGGAGTTCACCGAGCGCGACCTTCTCCCTGACGAAGTGGATGTC[G/A]
AGCTCGATGTGTTTGGTCCGCTTGTGGTGCACCGGATTCTTGGACATGTAGACGCTGGAGATGTTGTCACAGTAAGCGATCGTCGCCTGTGGAACGCGGC
GCCGCGTTCCACAGGCGACGATCGCTTACTGTGACAACATCTCCAGCGTCTACATGTCCAAGAATCCGGTGCACCACAAGCGGACCAAACACATCGAGCT[C/T]
GACATCCACTTCGTCAGGGAGAAGGTCGCGCTCGGTGAACTCCGCGTCCTACCGATACCGAGTGCCCATCAGTTCGCGGATGTGTTCACAAAAGGGCTTC
| 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 | 7.90% | 0.20% | 14.64% | 77.30% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 1.23% | 98.41% | NA |
| All Japonica | 1512 | 23.50% | 0.50% | 42.00% | 34.06% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.67% | 98.49% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.43% | 99.35% | NA |
| Indica III | 913 | 0.00% | 0.10% | 0.11% | 99.78% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 3.44% | 96.18% | NA |
| Temperate Japonica | 767 | 14.10% | 0.90% | 53.85% | 31.16% | NA |
| Tropical Japonica | 504 | 37.90% | 0.00% | 23.41% | 38.69% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 43.15% | 33.61% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 1.04% | 98.96% | NA |
| Intermediate | 90 | 10.00% | 0.00% | 24.44% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139403433 | G -> A | LOC_Os01g67800.1 | synonymous_variant ; p.Leu1351Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0139403433 | G -> DEL | LOC_Os01g67800.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |