| Variant ID: vg0324792824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24792824 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TACTTGCATGCACTCCCTCTAAGCAAAAGTATATCCTACTACTATCTGCTTCACAAAAGTACCCCTTTGTTTCACAAAAGTACTATCCTTCTATTTGCAT[G/A]
CCATCTATTTCACAAAAGTACTATCCTACTACTTGCATGCCATATGTTTCACAAAAGTACTCACTCTAATGCTGCGATTTCCTTTCTAATCCAAGCCAGG
CCTGGCTTGGATTAGAAAGGAAATCGCAGCATTAGAGTGAGTACTTTTGTGAAACATATGGCATGCAAGTAGTAGGATAGTACTTTTGTGAAATAGATGG[C/T]
ATGCAAATAGAAGGATAGTACTTTTGTGAAACAAAGGGGTACTTTTGTGAAGCAGATAGTAGTAGGATATACTTTTGCTTAGAGGGAGTGCATGCAAGTA
| 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 | 61.30% | 0.30% | 7.85% | 30.55% | NA |
| All Indica | 2759 | 37.30% | 0.00% | 11.85% | 50.85% | NA |
| All Japonica | 1512 | 98.90% | 0.50% | 0.00% | 0.60% | NA |
| Aus | 269 | 82.90% | 0.00% | 14.87% | 2.23% | NA |
| Indica I | 595 | 71.60% | 0.00% | 6.05% | 22.35% | NA |
| Indica II | 465 | 11.20% | 0.00% | 4.73% | 84.09% | NA |
| Indica III | 913 | 21.70% | 0.00% | 21.25% | 57.06% | NA |
| Indica Intermediate | 786 | 44.90% | 0.00% | 9.54% | 45.55% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 97.80% | 1.40% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 5.20% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 68.90% | 2.20% | 3.33% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324792824 | G -> A | LOC_Os03g44130.1 | 3_prime_UTR_variant ; 61.0bp to feature; MODIFIER | silent_mutation | Average:10.913; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0324792824 | G -> A | LOC_Os03g44140.1 | downstream_gene_variant ; 4980.0bp to feature; MODIFIER | silent_mutation | Average:10.913; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0324792824 | G -> DEL | N | N | silent_mutation | Average:10.913; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |