| Variant ID: vg0233354125 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 33354125 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )
AACTAAACTATAAAAAACTAGCTAATTACGCTTTTAAGCGATTTGGTATAATAATTGGTTGTAGCTTGTTGAATAAAGTCTGGAAATATATTCCATTATC[T/TA]
AAAAAAACTAGCTAATTAAATTAATCACCGTGAAAAAGCAGCTAAAGATCTTAGATCCTAGGTGTGAGATCTACATGGTACATCTTGGAAGGCTTGAGCC
GGCTCAAGCCTTCCAAGATGTACCATGTAGATCTCACACCTAGGATCTAAGATCTTTAGCTGCTTTTTCACGGTGATTAATTTAATTAGCTAGTTTTTTT[A/TA]
GATAATGGAATATATTTCCAGACTTTATTCAACAAGCTACAACCAATTATTATACCAAATCGCTTAAAAGCGTAATTAGCTAGTTTTTTATAGTTTAGTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.50% | 7.70% | 0.19% | 1.69% | NA |
| All Indica | 2759 | 93.80% | 3.00% | 0.25% | 2.90% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 3.70% | 95.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.30% | 0.00% | 0.00% | 1.68% | NA |
| Indica II | 465 | 97.20% | 0.60% | 0.43% | 1.72% | NA |
| Indica III | 913 | 91.30% | 4.40% | 0.55% | 3.72% | NA |
| Indica Intermediate | 786 | 91.20% | 5.20% | 0.00% | 3.56% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354125 | T -> TA | LOC_Os02g54450.1 | 3_prime_UTR_variant ; 50.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354125 | T -> TA | LOC_Os02g54430.1 | upstream_gene_variant ; 3126.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354125 | T -> TA | LOC_Os02g54440.1 | upstream_gene_variant ; 685.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354125 | T -> TA | LOC_Os02g54460.1 | upstream_gene_variant ; 2104.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354125 | T -> DEL | N | N | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |