| Variant ID: vg0412166795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12166795 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.54, A: 0.46, others allele: 0.00, population size: 107. )
AGACCGGCCAGGTTGAGTGGGCTCAATGATTGCCCTGTAACGGCTAGTTTTCTAGCCGTTACAAAGTAGTCCGGTCTGACCGGCCACTCTATGGCGGTCT[A/G]
ACCGGCAGAGCACAGAGTTGGGGATTTCGACATAACGGCTAGTTTTGGTGGTTGGGGGTATATATACCCACTCCCCAGCAGCAAGGGTAAGGTTTTGGCA
TGCCAAAACCTTACCCTTGCTGCTGGGGAGTGGGTATATATACCCCCAACCACCAAAACTAGCCGTTATGTCGAAATCCCCAACTCTGTGCTCTGCCGGT[T/C]
AGACCGCCATAGAGTGGCCGGTCAGACCGGACTACTTTGTAACGGCTAGAAAACTAGCCGTTACAGGGCAATCATTGAGCCCACTCAACCTGGCCGGTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.20% | 16.50% | 15.38% | 16.97% | NA |
| All Indica | 2759 | 76.40% | 1.50% | 19.72% | 2.39% | NA |
| All Japonica | 1512 | 3.20% | 47.50% | 5.82% | 43.52% | NA |
| Aus | 269 | 77.00% | 0.00% | 20.07% | 2.97% | NA |
| Indica I | 595 | 69.40% | 0.80% | 28.07% | 1.68% | NA |
| Indica II | 465 | 61.90% | 1.50% | 32.04% | 4.52% | NA |
| Indica III | 913 | 85.20% | 2.00% | 10.84% | 1.97% | NA |
| Indica Intermediate | 786 | 79.90% | 1.50% | 16.41% | 2.16% | NA |
| Temperate Japonica | 767 | 0.70% | 80.60% | 0.52% | 18.25% | NA |
| Tropical Japonica | 504 | 6.70% | 3.20% | 12.50% | 77.58% | NA |
| Japonica Intermediate | 241 | 3.70% | 34.90% | 8.71% | 52.70% | NA |
| VI/Aromatic | 96 | 22.90% | 2.10% | 22.92% | 52.08% | NA |
| Intermediate | 90 | 38.90% | 17.80% | 21.11% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412166795 | A -> DEL | N | N | silent_mutation | Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0412166795 | A -> G | LOC_Os04g21520.1 | upstream_gene_variant ; 4563.0bp to feature; MODIFIER | silent_mutation | Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0412166795 | A -> G | LOC_Os04g21510.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.979; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412166795 | NA | 5.67E-08 | mr1190 | 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 |
| vg0412166795 | 7.47E-07 | 3.30E-20 | mr1276 | 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 |
| vg0412166795 | NA | 7.15E-15 | mr1675 | 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 |
| vg0412166795 | NA | 3.19E-07 | mr1690 | 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 |
| vg0412166795 | NA | 4.75E-10 | mr1714 | 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 |