| Variant ID: vg0221167646 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21167646 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 227. )
TTTAAAGCACTCACAATGAAGTTAGCTTGCAACATATGGTTGAAGAGATAATATCCGCCAAAAAAAGGTTCATTGCATCATACACCTTGACGTAGGGAGA[T/C]
TAGTCTGTTCCTTTGTATAATAATTCATCTTTCGCTTTGGAGGTTTGAAATCTTGATAATAACTTCAAAAATGACTAGCTTTTCATTATTTCATCCAGAT
ATCTGGATGAAATAATGAAAAGCTAGTCATTTTTGAAGTTATTATCAAGATTTCAAACCTCCAAAGCGAAAGATGAATTATTATACAAAGGAACAGACTA[A/G]
TCTCCCTACGTCAAGGTGTATGATGCAATGAACCTTTTTTTGGCGGATATTATCTCTTCAACCATATGTTGCAAGCTAACTTCATTGTGAGTGCTTTAAA
| 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 | 66.10% | 33.70% | 0.15% | 0.08% | NA |
| All Indica | 2759 | 98.90% | 0.80% | 0.14% | 0.14% | NA |
| All Japonica | 1512 | 1.90% | 98.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.50% | 0.17% | 0.17% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.10% | 0.70% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 98.50% | 1.10% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 1.40% | 98.40% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.70% | 96.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 55.20% | 43.80% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 50.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221167646 | T -> DEL | N | N | silent_mutation | Average:51.042; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| vg0221167646 | T -> C | LOC_Os02g35200.1 | downstream_gene_variant ; 1960.0bp to feature; MODIFIER | silent_mutation | Average:51.042; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| vg0221167646 | T -> C | LOC_Os02g35220.1 | downstream_gene_variant ; 2883.0bp to feature; MODIFIER | silent_mutation | Average:51.042; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |
| vg0221167646 | T -> C | LOC_Os02g35210.1 | intron_variant ; MODIFIER | silent_mutation | Average:51.042; most accessible tissue: Minghui63 flag leaf, score: 68.675 | N | N | N | N |