| Variant ID: vg0517885731 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 17885731 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )
CAATTCTCTCAACCAACAAAAGGAGGAAGAAAAAGAAAGATACATACAGCTCTGTTTCTTCTCACCTTTCCCTACCAAATTATACCAACCATGATAAGCC[T/TA]
AAAAAAAATCATACATGGCATATCACAACAATGCAGAGCCTGTACAACTTCTAAGAAACAACAGCTGTTAGACTCTACAGACAATCATCATGTCATCAAA
TTTGATGACATGATGATTGTCTGTAGAGTCTAACAGCTGTTGTTTCTTAGAAGTTGTACAGGCTCTGCATTGTTGTGATATGCCATGTATGATTTTTTTT[A/TA]
GGCTTATCATGGTTGGTATAATTTGGTAGGGAAAGGTGAGAAGAAACAGAGCTGTATGTATCTTTCTTTTTCTTCCTCCTTTTGTTGGTTGAGAGAATTG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 35.20% | 0.06% | 0.36% | NA |
| All Indica | 2759 | 93.90% | 5.70% | 0.07% | 0.36% | NA |
| All Japonica | 1512 | 8.50% | 91.10% | 0.07% | 0.33% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 74.40% | 24.50% | 0.00% | 1.08% | NA |
| Indica III | 913 | 99.00% | 0.50% | 0.11% | 0.33% | NA |
| Indica Intermediate | 786 | 95.30% | 4.50% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 19.60% | 79.80% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 2.50% | 96.30% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 44.40% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517885731 | T -> DEL | N | N | silent_mutation | Average:58.124; most accessible tissue: Callus, score: 82.543 | N | N | N | N |
| vg0517885731 | T -> TA | LOC_Os05g30820.1 | 3_prime_UTR_variant ; 130.0bp to feature; MODIFIER | silent_mutation | Average:58.124; most accessible tissue: Callus, score: 82.543 | N | N | N | N |
| vg0517885731 | T -> TA | LOC_Os05g30810.1 | upstream_gene_variant ; 3484.0bp to feature; MODIFIER | silent_mutation | Average:58.124; most accessible tissue: Callus, score: 82.543 | N | N | N | N |
| vg0517885731 | T -> TA | LOC_Os05g30810.2 | upstream_gene_variant ; 3484.0bp to feature; MODIFIER | silent_mutation | Average:58.124; most accessible tissue: Callus, score: 82.543 | N | N | N | N |
| vg0517885731 | T -> TA | LOC_Os05g30820.2 | downstream_gene_variant ; 766.0bp to feature; MODIFIER | silent_mutation | Average:58.124; most accessible tissue: Callus, score: 82.543 | N | N | N | N |