| Variant ID: vg0203137419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3137419 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 111. )
GAGGTACTTCAGGTTCTGCCAGTTTCATTTGGAAGGAAGCTGGAATTTTTTTTCCCAATGTAATGAGTAGAGGGTATAGTCTGCCCAGTTTCAGGGTTTC[T/A]
CCCCCTCCAGTCGGAGGCTGTGCCTCGGACCATGCTCGACATGCTTTTGTCGATGTAACTATACTTTTGTACTTTGTTTTTTTTTTACTAATTCTTAATG
CATTAAGAATTAGTAAAAAAAAAACAAAGTACAAAAGTATAGTTACATCGACAAAAGCATGTCGAGCATGGTCCGAGGCACAGCCTCCGACTGGAGGGGG[A/T]
GAAACCCTGAAACTGGGCAGACTATACCCTCTACTCATTACATTGGGAAAAAAAATTCCAGCTTCCTTCCAAATGAAACTGGCAGAACCTGAAGTACCTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.60% | 7.00% | 0.19% | 2.14% | NA |
| All Indica | 2759 | 86.00% | 11.50% | 0.14% | 2.36% | NA |
| All Japonica | 1512 | 99.10% | 0.60% | 0.13% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 85.40% | 14.40% | 0.00% | 0.22% | NA |
| Indica III | 913 | 80.20% | 15.70% | 0.22% | 3.94% | NA |
| Indica Intermediate | 786 | 87.20% | 9.00% | 0.25% | 3.56% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 67.70% | 1.00% | 1.04% | 30.21% | NA |
| Intermediate | 90 | 90.00% | 4.40% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203137419 | T -> A | LOC_Os02g06270.1 | upstream_gene_variant ; 2434.0bp to feature; MODIFIER | silent_mutation | Average:58.869; most accessible tissue: Zhenshan97 flower, score: 79.196 | N | N | N | N |
| vg0203137419 | T -> A | LOC_Os02g06290.1 | upstream_gene_variant ; 4573.0bp to feature; MODIFIER | silent_mutation | Average:58.869; most accessible tissue: Zhenshan97 flower, score: 79.196 | N | N | N | N |
| vg0203137419 | T -> A | LOC_Os02g06290.2 | upstream_gene_variant ; 4875.0bp to feature; MODIFIER | silent_mutation | Average:58.869; most accessible tissue: Zhenshan97 flower, score: 79.196 | N | N | N | N |
| vg0203137419 | T -> A | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.869; most accessible tissue: Zhenshan97 flower, score: 79.196 | N | N | N | N |
| vg0203137419 | T -> DEL | N | N | silent_mutation | Average:58.869; most accessible tissue: Zhenshan97 flower, score: 79.196 | N | N | N | N |