| Variant ID: vg0801466220 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1466220 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.43, others allele: 0.00, population size: 84. )
CGTGGAGCAGCAGGCTAGCATGAGGTACCGGTATCTCGAGGTACTTTTTGTTGGACTGGAGCAAAATCTTTTTCTCCTATCTTACGTTTTTCCTATGCTA[T/C]
AATCCGAACAAGCCCTAAACTAGATTTCACCACGATAGCAAGATCTCAGGCCCTCCTGAGAAAGGATCCCTGCCCATAGCTAGGTATCCACAATTTTCTA
TAGAAAATTGTGGATACCTAGCTATGGGCAGGGATCCTTTCTCAGGAGGGCCTGAGATCTTGCTATCGTGGTGAAATCTAGTTTAGGGCTTGTTCGGATT[A/G]
TAGCATAGGAAAAACGTAAGATAGGAGAAAAAGATTTTGCTCCAGTCCAACAAAAAGTACCTCGAGATACCGGTACCTCATGCTAGCCTGCTGCTCCACG
| 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 | 36.30% | 10.70% | 1.29% | 51.74% | NA |
| All Indica | 2759 | 9.10% | 13.90% | 2.03% | 74.95% | NA |
| All Japonica | 1512 | 93.00% | 4.50% | 0.20% | 2.31% | NA |
| Aus | 269 | 1.50% | 14.50% | 0.00% | 84.01% | NA |
| Indica I | 595 | 9.90% | 2.40% | 2.52% | 85.21% | NA |
| Indica II | 465 | 4.70% | 11.00% | 1.72% | 82.58% | NA |
| Indica III | 913 | 8.40% | 19.90% | 1.75% | 69.88% | NA |
| Indica Intermediate | 786 | 12.00% | 17.30% | 2.16% | 68.58% | NA |
| Temperate Japonica | 767 | 88.30% | 8.70% | 0.39% | 2.61% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.40% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 9.40% | 3.10% | 1.04% | 86.46% | NA |
| Intermediate | 90 | 50.00% | 12.20% | 1.11% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801466220 | T -> C | LOC_Os08g03180.1 | upstream_gene_variant ; 2203.0bp to feature; MODIFIER | silent_mutation | Average:16.456; most accessible tissue: Callus, score: 91.032 | N | N | N | N |
| vg0801466220 | T -> C | LOC_Os08g03170.1 | downstream_gene_variant ; 127.0bp to feature; MODIFIER | silent_mutation | Average:16.456; most accessible tissue: Callus, score: 91.032 | N | N | N | N |
| vg0801466220 | T -> C | LOC_Os08g03160-LOC_Os08g03170 | intergenic_region ; MODIFIER | silent_mutation | Average:16.456; most accessible tissue: Callus, score: 91.032 | N | N | N | N |
| vg0801466220 | T -> DEL | N | N | silent_mutation | Average:16.456; most accessible tissue: Callus, score: 91.032 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0801466220 | NA | 2.51E-09 | mr1739 | Ind_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 |
| vg0801466220 | NA | 2.08E-06 | mr1758 | Ind_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 |
| vg0801466220 | NA | 1.83E-06 | mr1722_2 | Ind_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 |
| vg0801466220 | 7.90E-06 | 1.58E-08 | mr1758_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 |