| Variant ID: vg0620602697 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602697 |
| 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: 268. )
ACGTAGTGTTTAGGTAATTGTTATACAGTAATTGTTGCAACTTCTTTTTGAGCTGTCTGCTCCTCGGGGCGAATTCTATGAGCCACCTCCTTCAAGAGAG[A/G]
GCAAAGCAATGGTACACCTCTACTGTTGGATGTGTAAGCGGTAGTTGGGAGAAGTTGCGAGACAGATTCTGTCTTTCCTTCTTCCCAGTTACTCGTATTA
TAATACGAGTAACTGGGAAGAAGGAAAGACAGAATCTGTCTCGCAACTTCTCCCAACTACCGCTTACACATCCAACAGTAGAGGTGTACCATTGCTTTGC[T/C]
CTCTCTTGAAGGAGGTGGCTCATAGAATTCGCCCCGAGGAGCAGACAGCTCAAAAAGAAGTTGCAACAATTACTGTATAACAATTACCTAAACACTACGT
| 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 | 97.40% | 1.40% | 0.04% | 1.14% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.04% | 0.07% | NA |
| All Japonica | 1512 | 96.50% | 0.20% | 0.00% | 3.31% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.40% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 82.60% | 1.20% | 0.00% | 16.18% | NA |
| VI/Aromatic | 96 | 47.90% | 51.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 5.60% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602697 | A -> G | LOC_Os06g35340.1 | synonymous_variant ; p.Arg47Arg; LOW | synonymous_codon | Average:19.484; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
| vg0620602697 | A -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:19.484; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |