| Variant ID: vg0501385926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 1385926 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.02, others allele: 0.00, population size: 103. )
AGTTTGAAAAGTGTGCATGCGAAAAATAAGGTGATGAGTTGAAAAACCTGAGGTAAGAACAATATTTTTTGATGCCTAGAAATGGAACTGGAAAACCAAT[A/G]
TTTTTGAATTTCTTATCTTGGAAAATGATTGTCACATTTTTTTTGCACAATTCTAGATGTGTGTGCACATTAATTGTAAACATATGTATTTTTTGTCAAT
ATTGACAAAAAATACATATGTTTACAATTAATGTGCACACACATCTAGAATTGTGCAAAAAAAATGTGACAATCATTTTCCAAGATAAGAAATTCAAAAA[T/C]
ATTGGTTTTCCAGTTCCATTTCTAGGCATCAAAAAATATTGTTCTTACCTCAGGTTTTTCAACTCATCACCTTATTTTTCGCATGCACACTTTTCAAACT
| 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 | 72.40% | 27.40% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 53.90% | 45.80% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 27.10% | 72.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 39.10% | 60.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 83.50% | 15.80% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 48.50% | 51.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 17.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0501385926 | A -> G | LOC_Os05g03360.1 | upstream_gene_variant ; 2062.0bp to feature; MODIFIER | silent_mutation | Average:35.705; most accessible tissue: Callus, score: 87.409 | N | N | N | N |
| vg0501385926 | A -> G | LOC_Os05g03370.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.705; most accessible tissue: Callus, score: 87.409 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0501385926 | 5.54E-06 | 7.40E-08 | mr1510 | 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 |
| vg0501385926 | NA | 6.15E-16 | mr1807 | 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 |
| vg0501385926 | NA | 3.48E-06 | mr1807 | 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 |