| Variant ID: vg0518096322 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 18096322 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )
AGGCTTTTCCGACCAAAATTCGTGAGGCCGAATGGGCTCCGCACTCACCCTGATGAGCGTCGGCTATGAGCTCGATGCCCTGCTCTCGAGAAATACACTT[C/T]
AAGAGTATCCCGTTGGCGGCACGCCGGTATAGGGTCCCTTCTATAAGGACGTACCGTTTGGAGATGCGCGCGAGCTTTTCAACTTCTGCGCGATCCTCAG
CTGAGGATCGCGCAGAAGTTGAAAAGCTCGCGCGCATCTCCAAACGGTACGTCCTTATAGAAGGGACCCTATACCGGCGTGCCGCCAACGGGATACTCTT[G/A]
AAGTGTATTTCTCGAGAGCAGGGCATCGAGCTCATAGCCGACGCTCATCAGGGTGAGTGCGGAGCCCATTCGGCCTCACGAATTTTGGTCGGAAAAGCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.00% | 19.70% | 0.93% | 1.44% | NA |
| All Indica | 2759 | 93.20% | 3.30% | 1.16% | 2.28% | NA |
| All Japonica | 1512 | 50.90% | 48.30% | 0.66% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 76.80% | 11.40% | 1.51% | 10.32% | NA |
| Indica III | 913 | 97.00% | 1.60% | 1.10% | 0.22% | NA |
| Indica Intermediate | 786 | 93.40% | 3.10% | 1.91% | 1.65% | NA |
| Temperate Japonica | 767 | 77.70% | 21.90% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 21.40% | 77.40% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 27.40% | 71.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 85.40% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 27.80% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0518096322 | C -> T | LOC_Os05g31120.1 | downstream_gene_variant ; 226.0bp to feature; MODIFIER | silent_mutation | Average:64.132; most accessible tissue: Minghui63 flag leaf, score: 84.973 | N | N | N | N |
| vg0518096322 | C -> T | LOC_Os05g31130.1 | downstream_gene_variant ; 354.0bp to feature; MODIFIER | silent_mutation | Average:64.132; most accessible tissue: Minghui63 flag leaf, score: 84.973 | N | N | N | N |
| vg0518096322 | C -> T | LOC_Os05g31120-LOC_Os05g31130 | intergenic_region ; MODIFIER | silent_mutation | Average:64.132; most accessible tissue: Minghui63 flag leaf, score: 84.973 | N | N | N | N |
| vg0518096322 | C -> DEL | N | N | silent_mutation | Average:64.132; most accessible tissue: Minghui63 flag leaf, score: 84.973 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0518096322 | NA | 9.47E-06 | mr1044 | 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 |
| vg0518096322 | NA | 4.78E-08 | mr1408_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 |
| vg0518096322 | NA | 4.07E-07 | mr1554_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 |
| vg0518096322 | 3.45E-07 | NA | mr1758_2 | 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 |