| Variant ID: vg0233354124 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 33354124 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
AAACTAAACTATAAAAAACTAGCTAATTACGCTTTTAAGCGATTTGGTATAATAATTGGTTGTAGCTTGTTGAATAAAGTCTGGAAATATATTCCATTAT[C/CT]
TAAAAAAACTAGCTAATTAAATTAATCACCGTGAAAAAGCAGCTAAAGATCTTAGATCCTAGGTGTGAGATCTACATGGTACATCTTGGAAGGCTTGAGC
GCTCAAGCCTTCCAAGATGTACCATGTAGATCTCACACCTAGGATCTAAGATCTTTAGCTGCTTTTTCACGGTGATTAATTTAATTAGCTAGTTTTTTTA[G/AG]
ATAATGGAATATATTTCCAGACTTTATTCAACAAGCTACAACCAATTATTATACCAAATCGCTTAAAAGCGTAATTAGCTAGTTTTTTATAGTTTAGTTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 1.90% | 4.15% | 2.41% | NA |
| All Indica | 2759 | 94.60% | 3.30% | 1.49% | 0.62% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 13.40% | 0.00% | 54.28% | 32.34% | NA |
| Indica I | 595 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.20% | 0.00% | 0.43% | NA |
| Indica III | 913 | 93.00% | 4.60% | 1.75% | 0.66% | NA |
| Indica Intermediate | 786 | 92.10% | 3.60% | 3.18% | 1.15% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 2.08% | 6.25% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354124 | C -> CT | LOC_Os02g54450.1 | 3_prime_UTR_variant ; 51.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354124 | C -> CT | LOC_Os02g54430.1 | upstream_gene_variant ; 3125.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354124 | C -> CT | LOC_Os02g54440.1 | upstream_gene_variant ; 684.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354124 | C -> CT | LOC_Os02g54460.1 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |
| vg0233354124 | C -> DEL | N | N | silent_mutation | Average:59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 | N | N | N | N |