| Variant ID: vg0315011627 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15011627 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TATGTAAATATATAAAATATAAATCACACTTAAAGTATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGA[C/T]
AAATGGTCAAACATGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAAACGGAGGTAGTATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTC
GAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACATACTACCTCCGTTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACATGTTTGACCATTT[G/A]
TCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAATACTTTAAGTGTGATTTATATTTTATATATTTACATA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315011627 | C -> T | LOC_Os03g26240.1 | upstream_gene_variant ; 2174.0bp to feature; MODIFIER | N | Average:47.736; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0315011627 | C -> T | LOC_Os03g26260.1 | upstream_gene_variant ; 4179.0bp to feature; MODIFIER | N | Average:47.736; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0315011627 | C -> T | LOC_Os03g26229.1 | downstream_gene_variant ; 3367.0bp to feature; MODIFIER | N | Average:47.736; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0315011627 | C -> T | LOC_Os03g26250.1 | intron_variant ; MODIFIER | N | Average:47.736; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |