| Variant ID: vg0805183407 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5183407 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 96. )
CGGAGGAGGAGAGGCGGCGCCGAGAGAGAGGGAGGGAAGGGAAATGTTTTTAGGGTTAGGGTTTGGATCTTTGAACTTTTATATAGGTCGTGATCAATCA[G/A]
GACTGTCCATCAGATCGGACGGCTCAGCTTCTCCCGCGTTCCCAGGCTGCGCACACTATTGGGCCGCTTGTAATCTCCTCACAGAATAAGTTTACTTTAT
ATAAAGTAAACTTATTCTGTGAGGAGATTACAAGCGGCCCAATAGTGTGCGCAGCCTGGGAACGCGGGAGAAGCTGAGCCGTCCGATCTGATGGACAGTC[C/T]
TGATTGATCACGACCTATATAAAAGTTCAAAGATCCAAACCCTAACCCTAAAAACATTTCCCTTCCCTCCCTCTCTCTCGGCGCCGCCTCTCCTCCTCCG
| 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 | 81.50% | 15.90% | 0.13% | 2.45% | NA |
| All Indica | 2759 | 84.20% | 11.90% | 0.18% | 3.81% | NA |
| All Japonica | 1512 | 73.20% | 26.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 69.50% | 29.20% | 0.43% | 0.86% | NA |
| Indica III | 913 | 84.00% | 7.70% | 0.22% | 8.11% | NA |
| Indica Intermediate | 786 | 85.40% | 11.10% | 0.13% | 3.44% | NA |
| Temperate Japonica | 767 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 54.60% | 45.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 63.10% | 36.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 77.80% | 20.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0805183407 | G -> A | LOC_Os08g08910.1 | upstream_gene_variant ; 1886.0bp to feature; MODIFIER | silent_mutation | Average:69.593; most accessible tissue: Minghui63 root, score: 86.705 | N | N | N | N |
| vg0805183407 | G -> A | LOC_Os08g08920.1 | upstream_gene_variant ; 3468.0bp to feature; MODIFIER | silent_mutation | Average:69.593; most accessible tissue: Minghui63 root, score: 86.705 | N | N | N | N |
| vg0805183407 | G -> A | LOC_Os08g08910-LOC_Os08g08920 | intergenic_region ; MODIFIER | silent_mutation | Average:69.593; most accessible tissue: Minghui63 root, score: 86.705 | N | N | N | N |
| vg0805183407 | G -> DEL | N | N | silent_mutation | Average:69.593; most accessible tissue: Minghui63 root, score: 86.705 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805183407 | 8.17E-07 | 8.17E-07 | mr1440_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 |
| vg0805183407 | 4.76E-06 | 4.76E-06 | mr1453_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 |
| vg0805183407 | NA | 6.98E-06 | mr1556_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 |
| vg0805183407 | NA | 2.01E-07 | mr1646_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 |