| Variant ID: vg0409085829 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9085829 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCCATTAGTTTGGTTTAATTAAAAGAGAAAGGGAGGAGAACAGTTCTACTTTTCCAATATTTTTAGAGGGCTTCTATGGATAACCATTTGGCATAACCTA[G/C]
GGTCAAAGAGGCTCTGATACCAACTTGTCATGCCCGGAATTTCTATCCAAAATTCCAAACGCTTACATGTGTGTGAACCCTCGTCCAGGAATCAGCCGAG
CTCGGCTGATTCCTGGACGAGGGTTCACACACATGTAAGCGTTTGGAATTTTGGATAGAAATTCCGGGCATGACAAGTTGGTATCAGAGCCTCTTTGACC[C/G]
TAGGTTATGCCAAATGGTTATCCATAGAAGCCCTCTAAAAATATTGGAAAAGTAGAACTGTTCTCCTCCCTTTCTCTTTTAATTAAACCAAACTAATGGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.40% | 0.30% | 1.57% | 77.72% | NA |
| All Indica | 2759 | 0.80% | 0.50% | 1.05% | 97.64% | NA |
| All Japonica | 1512 | 60.80% | 0.10% | 2.25% | 36.84% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.74% | 98.88% | NA |
| Indica I | 595 | 0.50% | 0.30% | 0.84% | 98.32% | NA |
| Indica II | 465 | 1.30% | 0.20% | 0.22% | 98.28% | NA |
| Indica III | 913 | 0.30% | 1.10% | 1.53% | 97.04% | NA |
| Indica Intermediate | 786 | 1.30% | 0.10% | 1.15% | 97.46% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 4.20% | 0.20% | 5.95% | 89.68% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 1.66% | 30.29% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 7.29% | 91.67% | NA |
| Intermediate | 90 | 22.20% | 0.00% | 2.22% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409085829 | G -> C | LOC_Os04g16690.1 | downstream_gene_variant ; 3631.0bp to feature; MODIFIER | silent_mutation | Average:4.4; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409085829 | G -> C | LOC_Os04g16710.1 | downstream_gene_variant ; 3009.0bp to feature; MODIFIER | silent_mutation | Average:4.4; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409085829 | G -> C | LOC_Os04g16712.1 | downstream_gene_variant ; 4997.0bp to feature; MODIFIER | silent_mutation | Average:4.4; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409085829 | G -> C | LOC_Os04g16700.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.4; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409085829 | G -> DEL | N | N | silent_mutation | Average:4.4; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |