| Variant ID: vg0807402433 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7402433 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )
GATCACAGAGCATGGACGCCATGCAAACACAGGACGAATCGACATGTCCCGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATTCCTTTCAA[G/A]
AACTTATCAATAAAGGTAAGATTTAGCCATTCCGCTAGTTGCTGCTTATATATGTTGATTACTAATAAATAATCTCTCACAACATGAAGGTGGCGTCGGG
CCCGACGCCACCTTCATGTTGTGAGAGATTATTTATTAGTAATCAACATATATAAGCAGCAACTAGCGGAATGGCTAAATCTTACCTTTATTGATAAGTT[C/T]
TTGAAAGGAATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACGGGACATGTCGATTCGTCCTGTGTTTGCATGGCGTCCATGCTCTGTGATC
| 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 | 34.70% | 1.00% | 6.18% | 58.15% | NA |
| All Indica | 2759 | 15.00% | 1.40% | 4.89% | 78.65% | NA |
| All Japonica | 1512 | 76.90% | 0.40% | 6.15% | 16.53% | NA |
| Aus | 269 | 6.30% | 0.40% | 16.73% | 76.58% | NA |
| Indica I | 595 | 35.50% | 0.00% | 4.71% | 59.83% | NA |
| Indica II | 465 | 13.10% | 1.10% | 6.45% | 79.35% | NA |
| Indica III | 913 | 2.30% | 3.10% | 3.94% | 90.69% | NA |
| Indica Intermediate | 786 | 15.50% | 0.80% | 5.22% | 78.50% | NA |
| Temperate Japonica | 767 | 62.60% | 0.30% | 7.95% | 29.20% | NA |
| Tropical Japonica | 504 | 95.60% | 0.00% | 1.39% | 2.98% | NA |
| Japonica Intermediate | 241 | 83.40% | 1.70% | 10.37% | 4.56% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 16.67% | 76.04% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807402433 | G -> A | LOC_Os08g12500.1 | synonymous_variant ; p.Lys1416Lys; LOW | synonymous_codon | Average:6.255; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |
| vg0807402433 | G -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:6.255; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |