| Variant ID: vg0219101575 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 19101575 |
| 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: 340. )
TAGCTTCGTTCGAGTAGGGCTCATCTTTACCAGGGCATCTAACACCAGAGAAAGAGAAGGCAATGCTGCAAGTCTCCTTAGGAATTGTTAGTTTGAAACG[G/A]
TGGCCACTGAAGACATATTCAACAATTGCGGAATGTCTTCTGTTCCGCTGTAAGAAAGGAAGGAAGTCTCTGGCCTTCTTTGCTGAAACCTGAGCGCATA
TATGCGCTCAGGTTTCAGCAAAGAAGGCCAGAGACTTCCTTCCTTTCTTACAGCGGAACAGAAGACATTCCGCAATTGTTGAATATGTCTTCAGTGGCCA[C/T]
CGTTTCAAACTAACAATTCCTAAGGAGACTTGCAGCATTGCCTTCTCTTTCTCTGGTGTTAGATGCCCTGGTAAAGATGAGCCCTACTCGAACGAAGCTA
| 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 | 98.30% | 1.10% | 0.53% | 0.00% | NA |
| All Indica | 2759 | 97.20% | 1.90% | 0.87% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.00% | 2.50% | 2.52% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 2.70% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0219101575 | G -> A | LOC_Os02g32350.1 | synonymous_variant ; p.His598His; LOW | synonymous_codon | Average:72.164; most accessible tissue: Minghui63 flag leaf, score: 82.053 | N | N | N | N |
| vg0219101575 | G -> A | LOC_Os02g32350.2 | synonymous_variant ; p.His598His; LOW | synonymous_codon | Average:72.164; most accessible tissue: Minghui63 flag leaf, score: 82.053 | N | N | N | N |