| Variant ID: vg0210890398 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 10890398 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGACCCTGCACACCTCTGTAGTCAATTATCATACTATTTTTTGTGAAGTATAGCTACTATTCTTGATAACATATTATATGGAAATAATATTAGAAAATAA[A/G]
CATATTGTAATTGTTATTTAGAAAAGAGTGCACAGTGGCTCTATTTTGTGTAGACTTGACCATGCGAGTCAGTGTAGGATTTGATTGGTTGTAAGAATGA
TCATTCTTACAACCAATCAAATCCTACACTGACTCGCATGGTCAAGTCTACACAAAATAGAGCCACTGTGCACTCTTTTCTAAATAACAATTACAATATG[T/C]
TTATTTTCTAATATTATTTCCATATAATATGTTATCAAGAATAGTAGCTATACTTCACAAAAAATAGTATGATAATTGACTACAGAGGTGTGCAGGGTCT
| 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 | 83.00% | 12.70% | 4.32% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 0.10% | 1.59% | 0.00% | NA |
| All Japonica | 1512 | 52.10% | 38.20% | 9.72% | 0.00% | NA |
| Aus | 269 | 97.80% | 0.00% | 2.23% | 0.00% | NA |
| Indica I | 595 | 96.30% | 0.00% | 3.70% | 0.00% | NA |
| Indica II | 465 | 97.60% | 0.20% | 2.15% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 0.10% | 1.40% | 0.00% | NA |
| Temperate Japonica | 767 | 66.20% | 22.80% | 10.95% | 0.00% | NA |
| Tropical Japonica | 504 | 32.70% | 60.50% | 6.75% | 0.00% | NA |
| Japonica Intermediate | 241 | 47.30% | 40.70% | 12.03% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 12.20% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0210890398 | A -> G | LOC_Os02g18670.1 | upstream_gene_variant ; 4120.0bp to feature; MODIFIER | silent_mutation | Average:31.288; most accessible tissue: Minghui63 flag leaf, score: 43.614 | N | N | N | N |
| vg0210890398 | A -> G | LOC_Os02g18670-LOC_Os02g18690 | intergenic_region ; MODIFIER | silent_mutation | Average:31.288; most accessible tissue: Minghui63 flag leaf, score: 43.614 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0210890398 | 3.22E-06 | NA | mr1082 | 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 |
| vg0210890398 | 1.55E-06 | NA | mr1082 | 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 |
| vg0210890398 | 3.25E-06 | NA | mr1082_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 |