| Variant ID: vg0200790322 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 790322 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, TA: 0.21, others allele: 0.00, population size: 109. )
CACCTGATCATAAATTTCTCAAAACAATCAGCATCATGTAGATGAAATGGAACAATTGAAAATGCTCAATTTTGTTATTCTGTGACAGCTTGAGCTTTGT[T/TA]
TTTTTTAACTTAAAAGACGTTGTTTTGTCTGAATTTCAAGGTAAAGTTCAGCTACAAGTTAGAACTAGCTTGGTTTTGTATCATCCTGTTCATAGAGATT
AATCTCTATGAACAGGATGATACAAAACCAAGCTAGTTCTAACTTGTAGCTGAACTTTACCTTGAAATTCAGACAAAACAACGTCTTTTAAGTTAAAAAA[A/TA]
ACAAAGCTCAAGCTGTCACAGAATAACAAAATTGAGCATTTTCAATTGTTCCATTTCATCTACATGATGCTGATTGTTTTGAGAAATTTATGATCAGGTG
| 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 | 69.00% | 25.50% | 4.21% | 1.23% | NA |
| All Indica | 2759 | 57.10% | 41.00% | 1.52% | 0.43% | NA |
| All Japonica | 1512 | 82.90% | 4.10% | 10.12% | 2.91% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 66.90% | 32.40% | 0.50% | 0.17% | NA |
| Indica II | 465 | 58.70% | 34.60% | 4.95% | 1.72% | NA |
| Indica III | 913 | 41.10% | 58.60% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 67.30% | 30.70% | 1.65% | 0.38% | NA |
| Temperate Japonica | 767 | 96.20% | 0.30% | 2.35% | 1.17% | NA |
| Tropical Japonica | 504 | 61.50% | 7.10% | 24.80% | 6.55% | NA |
| Japonica Intermediate | 241 | 85.10% | 10.00% | 4.15% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 15.60% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200790322 | T -> TA | LOC_Os02g02350.2 | upstream_gene_variant ; 4647.0bp to feature; MODIFIER | silent_mutation | Average:64.723; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790322 | T -> TA | LOC_Os02g02360.1 | downstream_gene_variant ; 1088.0bp to feature; MODIFIER | silent_mutation | Average:64.723; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790322 | T -> TA | LOC_Os02g02380.1 | downstream_gene_variant ; 4743.0bp to feature; MODIFIER | silent_mutation | Average:64.723; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790322 | T -> TA | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.723; most accessible tissue: Callus, score: 84.374 | N | N | N | N |
| vg0200790322 | T -> DEL | N | N | silent_mutation | Average:64.723; most accessible tissue: Callus, score: 84.374 | N | N | N | N |