| Variant ID: vg0209333893 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9333893 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACGTGCGTGTATTATTCCTTGTCCCAGGAGGCAAGGTACACCAAAAGTTGATACAATTCAGAGTTTAACAAGCGGAAGCGTAAATAGTTATTTATTACAT[G/A]
GGCAGCGACGGCCCAGCACACTCAAAGACAACGAAAAACAGCAGAAGACTAAGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAG
CTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCTTAGTCTTCTGCTGTTTTTCGTTGTCTTTGAGTGTGCTGGGCCGTCGCTGCC[C/T]
ATGTAATAAATAACTATTTACGCTTCCGCTTGTTAAACTCTGAATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGGACAAGGAATAATACACGCACGT
| 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 | 51.50% | 0.10% | 2.86% | 45.56% | NA |
| All Indica | 2759 | 26.60% | 0.20% | 4.24% | 68.90% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.07% | 2.51% | NA |
| Aus | 269 | 30.10% | 0.00% | 4.83% | 65.06% | NA |
| Indica I | 595 | 26.20% | 0.00% | 2.18% | 71.60% | NA |
| Indica II | 465 | 29.70% | 0.20% | 5.16% | 64.95% | NA |
| Indica III | 913 | 23.50% | 0.30% | 4.60% | 71.52% | NA |
| Indica Intermediate | 786 | 28.80% | 0.30% | 4.83% | 66.16% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.60% | 0.00% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333893 | G -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1937.0bp to feature; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333893 | G -> A | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333893 | G -> DEL | N | N | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |