| Variant ID: vg0233334543 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33334543 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 76. )
TTCTCTCCATTTGCCGCGGACCAAATGACGGAACCGATACCAAGCCCTACATGGAGTTTAAAGCTATGATTCGTAGTAGCAATTAACATAACAAGACTTT[C/A]
TTAATTAACAAAGGAACTTATGACGGTACCTGTCTATAAGTTCGAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGT
ACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTCGAACTTATAGACAGGTACCGTCATAAGTTCCTTTGTTAATTAA[G/T]
AAAGTCTTGTTATGTTAATTGCTACTACGAATCATAGCTTTAAACTCCATGTAGGGCTTGGTATCGGTTCCGTCATTTGGTCCGCGGCAAATGGAGAGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.90% | 0.10% | 0.72% | 63.25% | NA |
| All Indica | 2759 | 2.00% | 0.00% | 0.65% | 97.32% | NA |
| All Japonica | 1512 | 98.70% | 0.30% | 0.20% | 0.79% | NA |
| Aus | 269 | 3.00% | 0.00% | 4.09% | 92.94% | NA |
| Indica I | 595 | 1.20% | 0.00% | 0.34% | 98.49% | NA |
| Indica II | 465 | 3.00% | 0.00% | 0.43% | 96.56% | NA |
| Indica III | 913 | 0.90% | 0.00% | 1.20% | 97.92% | NA |
| Indica Intermediate | 786 | 3.40% | 0.00% | 0.38% | 96.18% | NA |
| Temperate Japonica | 767 | 98.20% | 0.70% | 0.39% | 0.78% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233334543 | C -> A | LOC_Os02g54390.1 | upstream_gene_variant ; 3111.0bp to feature; MODIFIER | silent_mutation | Average:6.222; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0233334543 | C -> A | LOC_Os02g54400.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.222; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0233334543 | C -> DEL | N | N | silent_mutation | Average:6.222; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |