| Variant ID: vg0521668114 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 21668114 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 130. )
TGTCTGAACAAGTCATCACATAAATACTCTATTCCGGCCGTATGCATTTTGTCTCTCGCCTGTTCAATCACACCAAAAGTTGATAAGTATATTTTGTTGG[A/AT]
TTTTATTGTTCCTGGCAATGATTCAATTGCTCTTGTCAAAAATTGCATCAACAATTAATTCAACAAACGCTACAATTTGATTTTCAGCAGGCTTTTATTA
TAATAAAAGCCTGCTGAAAATCAAATTGTAGCGTTTGTTGAATTAATTGTTGATGCAATTTTTGACAAGAGCAATTGAATCATTGCCAGGAACAATAAAA[T/AT]
CCAACAAAATATACTTATCAACTTTTGGTGTGATTGAACAGGCGAGAGACAAAATGCATACGGCCGGAATAGAGTATTTATGTGATGACTTGTTCAGACA
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.00% | 36.90% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 98.10% | 1.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 1.50% | 98.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 75.10% | 24.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.40% | 3.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 1.40% | 98.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 51.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0521668114 | A -> AT | LOC_Os05g37080.1 | 3_prime_UTR_variant ; 289.0bp to feature; MODIFIER | silent_mutation | Average:52.111; most accessible tissue: Minghui63 flower, score: 74.23 | N | N | N | N |
| vg0521668114 | A -> AT | LOC_Os05g37070.1 | upstream_gene_variant ; 2544.0bp to feature; MODIFIER | silent_mutation | Average:52.111; most accessible tissue: Minghui63 flower, score: 74.23 | N | N | N | N |