| Variant ID: vg0221218849 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21218849 |
| 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: 254. )
ATCAAATATAATGACGAAGTTGCCCATCAAACAGCAGTAGAATAGGGCTATGTTGAAAAGGCTTGACAGGATATTGATGAAGATGACGATGTCGGTGATC[C/T]
CGTCAATAGCAGTGTAGCAACCGATGATAATGATGAAGACGCTCATCAGCGTTTGCAAAGTAGGTCAACCGTGAGGGCGAAATAACAAGTCGGCAATGAC
GTCATTGCCGACTTGTTATTTCGCCCTCACGGTTGACCTACTTTGCAAACGCTGATGAGCGTCTTCATCATTATCATCGGTTGCTACACTGCTATTGACG[G/A]
GATCACCGACATCGTCATCTTCATCAATATCCTGTCAAGCCTTTTCAACATAGCCCTATTCTACTGCTGTTTGATGGGCAACTTCGTCATTATATTTGAT
| 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 | 52.80% | 46.70% | 0.53% | 0.00% | NA |
| All Indica | 2759 | 22.90% | 76.40% | 0.76% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 1.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 80.70% | 18.20% | 1.12% | 0.00% | NA |
| Indica I | 595 | 6.90% | 92.60% | 0.50% | 0.00% | NA |
| Indica II | 465 | 20.00% | 79.40% | 0.65% | 0.00% | NA |
| Indica III | 913 | 35.20% | 64.10% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 22.40% | 76.60% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 1.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 30.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221218849 | C -> T | LOC_Os02g35290-LOC_Os02g35300 | intergenic_region ; MODIFIER | silent_mutation | Average:16.694; most accessible tissue: Minghui63 flower, score: 21.909 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0221218849 | NA | 5.24E-07 | mr1220 | 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 |
| vg0221218849 | 8.81E-06 | 1.94E-06 | mr1908 | 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 |
| vg0221218849 | NA | 4.47E-06 | mr1438_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 |