| Variant ID: vg0614963104 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14963104 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 241. )
TCAACATAAGTAATAAATGTTCATAAGCGAATTACTAACACATATTAAACAAGAGTACAAACAAACAAAAGTGTTTAGTCCGAACACTCATCACGATAAC[A/G]
TTATGATACAACACCGAATAGTTCGCAATACTACTAGTACAACAATAGTCGGAGGTACTCATTACAACAAGATTGAATTGAAATTACACGATAGAAGTAT
ATACTTCTATCGTGTAATTTCAATTCAATCTTGTTGTAATGAGTACCTCCGACTATTGTTGTACTAGTAGTATTGCGAACTATTCGGTGTTGTATCATAA[T/C]
GTTATCGTGATGAGTGTTCGGACTAAACACTTTTGTTTGTTTGTACTCTTGTTTAATATGTGTTAGTAATTCGCTTATGAACATTTATTACTTATGTTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.00% | 5.60% | 6.90% | 58.51% | NA |
| All Indica | 2759 | 2.90% | 7.40% | 3.48% | 86.23% | NA |
| All Japonica | 1512 | 79.60% | 0.80% | 2.78% | 16.87% | NA |
| Aus | 269 | 12.30% | 14.10% | 45.35% | 28.25% | NA |
| Indica I | 595 | 5.00% | 0.80% | 1.51% | 92.61% | NA |
| Indica II | 465 | 1.70% | 1.10% | 1.94% | 95.27% | NA |
| Indica III | 913 | 0.80% | 14.60% | 4.82% | 79.85% | NA |
| Indica Intermediate | 786 | 4.60% | 7.60% | 4.33% | 83.46% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.39% | 3.39% | NA |
| Tropical Japonica | 504 | 51.20% | 2.00% | 7.14% | 39.68% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 1.24% | 12.03% | NA |
| VI/Aromatic | 96 | 28.10% | 8.30% | 51.04% | 12.50% | NA |
| Intermediate | 90 | 27.80% | 5.60% | 18.89% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614963104 | A -> G | LOC_Os06g25580.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.835; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614963104 | A -> DEL | N | N | silent_mutation | Average:4.835; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |