| Variant ID: vg0605309659 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 5309659 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCTATTTCATAGTATTAATAGTAGTATGCACAAGAAATAAACGTGCTGATTCAGTCAAAGATTTTTTTAGAAAATAGTATACCTGGAGTAACTTCACGA[T/C]
GTCGCCTCATGATATATTGGATCTAGCGATGGCAATGGAGCCCCGTTGCCACCCCGGATTTGATCAGGTTATTTTCGGTGGTGTCATATGGTGTTTCATC
GATGAAACACCATATGACACCACCGAAAATAACCTGATCAAATCCGGGGTGGCAACGGGGCTCCATTGCCATCGCTAGATCCAATATATCATGAGGCGAC[A/G]
TCGTGAAGTTACTCCAGGTATACTATTTTCTAAAAAAATCTTTGACTGAATCAGCACGTTTATTTCTTGTGCATACTACTATTAATACTATGAAATAGAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.40% | 0.46% | 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 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.20% | 0.40% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0605309659 | T -> C | LOC_Os06g10320.1 | downstream_gene_variant ; 2928.0bp to feature; MODIFIER | silent_mutation | Average:64.629; most accessible tissue: Minghui63 flower, score: 76.374 | N | N | N | N |
| vg0605309659 | T -> C | LOC_Os06g10330.1 | downstream_gene_variant ; 1912.0bp to feature; MODIFIER | silent_mutation | Average:64.629; most accessible tissue: Minghui63 flower, score: 76.374 | N | N | N | N |
| vg0605309659 | T -> C | LOC_Os06g10340.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.629; most accessible tissue: Minghui63 flower, score: 76.374 | N | N | N | N |