| Variant ID: vg0315011650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011650 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCACACTTAAAGTATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACATGTGAGAAA[A/T]
AGTCAACGGCGTCATCTATTAAAAAAACGGAGGTAGTATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGACAAATCGGA
TCCGATTTGTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACATACTACCTCCGTTTTTTTAATAGATGACGCCGTTGACT[T/A]
TTTCTCACATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAATACTTTAAGTGTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.50% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 0.90% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.70% | 0.50% | 0.00% | NA |
| Indica II | 465 | 97.20% | 1.70% | 1.08% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.40% | 0.38% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011650 | A -> T | LOC_Os03g26240.1 | upstream_gene_variant ; 2197.0bp to feature; MODIFIER | N | Average:39.847; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011650 | A -> T | LOC_Os03g26260.1 | upstream_gene_variant ; 4156.0bp to feature; MODIFIER | N | Average:39.847; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011650 | A -> T | LOC_Os03g26229.1 | downstream_gene_variant ; 3390.0bp to feature; MODIFIER | N | Average:39.847; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0315011650 | A -> T | LOC_Os03g26250.1 | intron_variant ; MODIFIER | N | Average:39.847; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |