| Variant ID: vg0517888098 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 17888098 |
| Reference Allele: T | Alternative Allele: TA,TAA |
| 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: 300. )
AAGGAGACACCGAAAGAATCCAGACAACATACAAACACATGAGGAACAATTAAGACCAACACAGTTCAAGCTCAGGACACAGCTAAATTCCATTCTTCTA[T/TA,TAA]
AAAAAAAAAGGAGTTCCAATCTTTCCCCCCCAACAACAATATCACCCTGATTCTGCATCCACATTTTACCTCTTCAGCGAATTCCTGCCTCGGCGCCCCA
TGGGGCGCCGAGGCAGGAATTCGCTGAAGAGGTAAAATGTGGATGCAGAATCAGGGTGATATTGTTGTTGGGGGGGAAAGATTGGAACTCCTTTTTTTTT[A/TA,TTA]
TAGAAGAATGGAATTTAGCTGTGTCCTGAGCTTGAACTGTGTTGGTCTTAATTGTTCCTCATGTGTTTGTATGTTGTCTGGATTCTTTCGGTGTCTCCTT
| 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 | 87.70% | 11.90% | 0.04% | 0.00% | TAA: 0.30% |
| All Indica | 2759 | 99.10% | 0.90% | 0.04% | 0.00% | TAA: 0.04% |
| All Japonica | 1512 | 64.60% | 35.10% | 0.00% | 0.00% | TAA: 0.26% |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.00% | TAA: 0.74% |
| Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 1.30% | 0.00% | 0.00% | TAA: 0.13% |
| Temperate Japonica | 767 | 37.90% | 61.90% | 0.00% | 0.00% | TAA: 0.13% |
| Tropical Japonica | 504 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.00% | 10.80% | 0.00% | 0.00% | TAA: 1.24% |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 0.00% | TAA: 4.17% |
| Intermediate | 90 | 85.60% | 10.00% | 1.11% | 0.00% | TAA: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517888098 | T -> TA | LOC_Os05g30830.1 | downstream_gene_variant ; 3870.0bp to feature; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |
| vg0517888098 | T -> TA | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |
| vg0517888098 | T -> TA | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |
| vg0517888098 | T -> TAA | LOC_Os05g30830.1 | downstream_gene_variant ; 3870.0bp to feature; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |
| vg0517888098 | T -> TAA | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |
| vg0517888098 | T -> TAA | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.087; most accessible tissue: Zhenshan97 flower, score: 83.061 | N | N | N | N |