| Variant ID: vg0417168684 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 17168684 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )
GTCGTCGATTGGTGTCCTCGCCTACATGGTTGGTTGGTCACACCACCATTGTTGGACATCCACGTCTTTATCACCGGCCTATCTTCATCACCGTCGATGG[C/A]
ATTTTATCTTCACCACCGGCCGCTATCTCAGCTACTTCCACGGTTGGTATCTTCGTCACCATTGATGGACGATATTGTTCCCACATCGGCCACTTCTGTT
AACAGAAGTGGCCGATGTGGGAACAATATCGTCCATCAATGGTGACGAAGATACCAACCGTGGAAGTAGCTGAGATAGCGGCCGGTGGTGAAGATAAAAT[G/T]
CCATCGACGGTGATGAAGATAGGCCGGTGATAAAGACGTGGATGTCCAACAATGGTGGTGTGACCAACCAACCATGTAGGCGAGGACACCAATCGACGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.70% | 5.30% | 1.95% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 0.40% | 0.94% | 0.00% | NA |
| All Japonica | 1512 | 80.40% | 15.50% | 4.10% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.50% | 0.00% | 2.52% | 0.00% | NA |
| Indica II | 465 | 97.80% | 1.70% | 0.43% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 0.30% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 65.20% | 28.40% | 6.39% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 0.20% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.10% | 6.20% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 8.90% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0417168684 | C -> A | LOC_Os04g28970.1 | downstream_gene_variant ; 4730.0bp to feature; MODIFIER | silent_mutation | Average:57.006; most accessible tissue: Zhenshan97 young leaf, score: 73.147 | N | N | N | N |
| vg0417168684 | C -> A | LOC_Os04g28940-LOC_Os04g28970 | intergenic_region ; MODIFIER | silent_mutation | Average:57.006; most accessible tissue: Zhenshan97 young leaf, score: 73.147 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0417168684 | 2.79E-06 | 2.79E-06 | mr1060 | Jap_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 |
| vg0417168684 | NA | 6.35E-07 | mr1521 | Jap_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 |
| vg0417168684 | NA | 2.86E-07 | mr1668 | Jap_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 |