| Variant ID: vg0608663055 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8663055 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.26, others allele: 0.00, population size: 94. )
TCTTTTCTTTCGCCCAAGCAAGTACCTCTGCAAACGAAAACACACAAAACTCATTGTATAGCAACGTTTGTTCAAATATATAACAAGTAAATCTAATATA[A/G]
AACGTATGCACCTTTATTTGATTAATACATAAGGTAGTCATGGTTATATCCGAGCTAGTTGTGTTCTCATGACCTAGAGATTGGCGAAATGTTGCATAGC
GCTATGCAACATTTCGCCAATCTCTAGGTCATGAGAACACAACTAGCTCGGATATAACCATGACTACCTTATGTATTAATCAAATAAAGGTGCATACGTT[T/C]
TATATTAGATTTACTTGTTATATATTTGAACAAACGTTGCTATACAATGAGTTTTGTGTGTTTTCGTTTGCAGAGGTACTTGCTTGGGCGAAAGAAAAGA
| 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 | 42.80% | 21.60% | 0.70% | 34.87% | NA |
| All Indica | 2759 | 5.40% | 35.20% | 1.20% | 58.25% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.00% | 0.79% | NA |
| Aus | 269 | 85.50% | 13.80% | 0.00% | 0.74% | NA |
| Indica I | 595 | 2.70% | 40.70% | 0.67% | 55.97% | NA |
| Indica II | 465 | 4.90% | 16.10% | 1.72% | 77.20% | NA |
| Indica III | 913 | 4.50% | 50.20% | 0.66% | 44.69% | NA |
| Indica Intermediate | 786 | 8.80% | 24.80% | 1.91% | 64.50% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 11.10% | 0.00% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0608663055 | A -> G | LOC_Os06g15260.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.55; most accessible tissue: Zhenshan97 young leaf, score: 53.969 | N | N | N | N |
| vg0608663055 | A -> DEL | N | N | silent_mutation | Average:34.55; most accessible tissue: Zhenshan97 young leaf, score: 53.969 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608663055 | NA | 2.10E-13 | mr1655 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0608663055 | NA | 1.36E-36 | mr1181_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0608663055 | NA | 2.58E-06 | mr1181_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |