| Variant ID: vg0104863244 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 4863244 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 53. )
CGGTGTCCCCCGGCCGGGCTCGGTACGGCTGGCCACGGGCGACGGCACGGAGCTGCCAAACCCGTGGAACATCGAACACCTTCGCCGCTTCTACCCCTGA[A/G]
AGGGGGGGTCGGGTGTCAGGTTTCTATCTCGGGCCAACCCCGCACCCCCCTCGGGTGTGCAGGGTTGGCCGGGGGCTACCACACATGCACATATATTCCT
AGGAATATATGTGCATGTGTGGTAGCCCCCGGCCAACCCTGCACACCCGAGGGGGGTGCGGGGTTGGCCCGAGATAGAAACCTGACACCCGACCCCCCCT[T/C]
TCAGGGGTAGAAGCGGCGAAGGTGTTCGATGTTCCACGGGTTTGGCAGCTCCGTGCCGTCGCCCGTGGCCAGCCGTACCGAGCCCGGCCGGGGGACACCG
| 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 | 12.80% | 2.80% | 8.93% | 75.48% | NA |
| All Indica | 2759 | 1.60% | 3.20% | 11.71% | 83.47% | NA |
| All Japonica | 1512 | 35.20% | 0.50% | 0.86% | 63.49% | NA |
| Aus | 269 | 0.00% | 10.40% | 5.95% | 83.64% | NA |
| Indica I | 595 | 0.80% | 1.80% | 18.32% | 78.99% | NA |
| Indica II | 465 | 3.00% | 3.40% | 6.45% | 87.10% | NA |
| Indica III | 913 | 2.00% | 3.90% | 9.75% | 84.34% | NA |
| Indica Intermediate | 786 | 1.00% | 3.20% | 12.09% | 83.72% | NA |
| Temperate Japonica | 767 | 59.20% | 0.00% | 0.26% | 40.55% | NA |
| Tropical Japonica | 504 | 2.60% | 1.40% | 1.59% | 94.44% | NA |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 1.24% | 71.78% | NA |
| VI/Aromatic | 96 | 17.70% | 4.20% | 57.29% | 20.83% | NA |
| Intermediate | 90 | 14.40% | 3.30% | 16.67% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0104863244 | A -> G | LOC_Os01g09530.1 | downstream_gene_variant ; 634.0bp to feature; MODIFIER | silent_mutation | Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0104863244 | A -> G | LOC_Os01g09520.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0104863244 | A -> DEL | N | N | silent_mutation | Average:18.163; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0104863244 | NA | 9.70E-07 | mr1057_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 |
| vg0104863244 | NA | 1.52E-06 | mr1363_2 | 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 |
| vg0104863244 | NA | 8.26E-06 | mr1577_2 | 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 |
| vg0104863244 | NA | 2.14E-06 | mr1840_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 |