| Variant ID: vg0209333899 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9333899 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGTATTATTCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATTCAGAGTTTAACAAGCGGAAGCGTAAATAGTTATTTATTACATGGGCAG[C/T]
GACGGCCCAGCACACTCAAAGACAACGAAAAACAGCAGAAGACTAAGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCA
TGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCTTAGTCTTCTGCTGTTTTTCGTTGTCTTTGAGTGTGCTGGGCCGTC[G/A]
CTGCCCATGTAATAAATAACTATTTACGCTTCCGCTTGTTAAACTCTGAATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGAATAATACAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.20% | 0.20% | 3.58% | 45.05% | NA |
| All Indica | 2759 | 27.40% | 0.10% | 4.78% | 67.78% | NA |
| All Japonica | 1512 | 97.20% | 0.00% | 0.20% | 2.58% | NA |
| Aus | 269 | 19.00% | 2.20% | 11.52% | 67.29% | NA |
| Indica I | 595 | 27.70% | 0.00% | 2.69% | 69.58% | NA |
| Indica II | 465 | 32.50% | 0.00% | 3.87% | 63.66% | NA |
| Indica III | 913 | 22.30% | 0.10% | 5.37% | 72.18% | NA |
| Indica Intermediate | 786 | 29.90% | 0.10% | 6.23% | 63.74% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.00% | 0.00% | 0.40% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 2.22% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333899 | C -> T | LOC_Os02g16390.1 | upstream_gene_variant ; 1931.0bp to feature; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333899 | C -> T | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333899 | C -> DEL | N | N | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |