| Variant ID: vg0318608283 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18608283 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGCCAGTTCTGCCCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACACACACACACTGTTAAATAAACCGACAGCAAATT[G/A,T]
GGGGGGCAACACGAAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGC
GCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTTCGTGTTGCCCCCC[C/T,A]
AATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGGGCAGAACTGGCAG
| 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 | 92.00% | 2.40% | 5.46% | 0.04% | T: 0.02% |
| All Indica | 2759 | 87.60% | 4.10% | 8.30% | 0.00% | NA |
| All Japonica | 1512 | 98.30% | 0.10% | 1.46% | 0.13% | T: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.20% | 1.34% | 0.00% | NA |
| Indica II | 465 | 90.50% | 1.90% | 7.53% | 0.00% | NA |
| Indica III | 913 | 78.50% | 7.30% | 14.13% | 0.00% | NA |
| Indica Intermediate | 786 | 88.20% | 4.60% | 7.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 4.17% | 0.40% | T: 0.20% |
| 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 | 91.10% | 1.10% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318608283 | G -> T | LOC_Os03g32540.1 | upstream_gene_variant ; 2910.0bp to feature; MODIFIER | silent_mutation | Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608283 | G -> T | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608283 | G -> A | LOC_Os03g32540.1 | upstream_gene_variant ; 2910.0bp to feature; MODIFIER | silent_mutation | Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608283 | G -> A | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0318608283 | G -> DEL | N | N | silent_mutation | Average:22.085; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |