| Variant ID: vg1216386947 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16386947 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )
ATGTATCTTGTTTTCGAAAGGAAGTCCATCAAAAGCTCTAGCAATGTGAGGGTTGGCAACCAAATGAGCATAGTAAACAGATACATGGATCTCCTCAAAC[C/T]
CAGGAAGGCTTTTCAAGGTTTGAAATAAACCATCTGGCAGTTTATTGTCTGGCTCAGCGACCTTTAGTATAGCAGAAGCTAACTTGTCACCAACACTGGT
ACCAGTGTTGGTGACAAGTTAGCTTCTGCTATACTAAAGGTCGCTGAGCCAGACAATAAACTGCCAGATGGTTTATTTCAAACCTTGAAAAGCCTTCCTG[G/A]
GTTTGAGGAGATCCATGTATCTGTTTACTATGCTCATTTGGTTGCCAACCCTCACATTGCTAGAGCTTTTGATGGACTTCCTTTCGAAAACAAGATACAT
| 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 | 98.80% | 0.00% | 0.53% | 0.68% | NA |
| All Indica | 2759 | 98.10% | 0.00% | 0.91% | 0.94% | NA |
| All Japonica | 1512 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.00% | 2.18% | 0.34% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.22% | 0.86% | NA |
| Indica III | 913 | 98.50% | 0.10% | 0.44% | 0.99% | NA |
| Indica Intermediate | 786 | 97.70% | 0.00% | 0.89% | 1.40% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216386947 | C -> T | LOC_Os12g27800.1 | missense_variant ; p.Gly534Glu; MODERATE | N | Average:11.73; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216386947 | C -> T | LOC_Os12g27810.1 | upstream_gene_variant ; 4478.0bp to feature; MODIFIER | N | Average:11.73; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216386947 | C -> T | LOC_Os12g27790.1 | downstream_gene_variant ; 2925.0bp to feature; MODIFIER | N | Average:11.73; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |