| Variant ID: vg1121803238 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21803238 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 104. )
TTATCAGGGTGCTAGCCGATAAGTTAATGCTAGTGTTTTATCGGGGTGCTAGCCGATAAGTTATCTGGACATTGCATCGGCTTACAAAGATTACATACAA[A/G]
TTGGATTTAGCCGATTGCAACAAAGGTTTCACTGTTTATCTAAATTGATTGGATTTTATGACATCGGAATTTTAGCCGATGTATGCTTTAACCATCGAAT
ATTCGATGGTTAAAGCATACATCGGCTAAAATTCCGATGTCATAAAATCCAATCAATTTAGATAAACAGTGAAACCTTTGTTGCAATCGGCTAAATCCAA[T/C]
TTGTATGTAATCTTTGTAAGCCGATGCAATGTCCAGATAACTTATCGGCTAGCACCCCGATAAAACACTAGCATTAACTTATCGGCTAGCACCCTGATAA
| 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 | 69.40% | 24.90% | 2.18% | 3.60% | NA |
| All Indica | 2759 | 64.90% | 26.60% | 3.01% | 5.44% | NA |
| All Japonica | 1512 | 78.30% | 19.40% | 1.12% | 1.19% | NA |
| Aus | 269 | 79.60% | 20.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 73.80% | 22.00% | 2.35% | 1.85% | NA |
| Indica II | 465 | 60.60% | 29.50% | 4.95% | 4.95% | NA |
| Indica III | 913 | 62.70% | 28.00% | 1.64% | 7.67% | NA |
| Indica Intermediate | 786 | 63.40% | 26.80% | 3.94% | 5.85% | NA |
| Temperate Japonica | 767 | 94.30% | 3.90% | 1.04% | 0.78% | NA |
| Tropical Japonica | 504 | 51.80% | 46.00% | 0.79% | 1.39% | NA |
| Japonica Intermediate | 241 | 83.00% | 12.90% | 2.07% | 2.07% | NA |
| VI/Aromatic | 96 | 27.10% | 69.80% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 70.00% | 27.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1121803238 | A -> DEL | N | N | silent_mutation | Average:21.101; most accessible tissue: Callus, score: 34.153 | N | N | N | N |
| vg1121803238 | A -> G | LOC_Os11g36960.1 | upstream_gene_variant ; 2861.0bp to feature; MODIFIER | silent_mutation | Average:21.101; most accessible tissue: Callus, score: 34.153 | N | N | N | N |
| vg1121803238 | A -> G | LOC_Os11g36950.1 | downstream_gene_variant ; 4789.0bp to feature; MODIFIER | silent_mutation | Average:21.101; most accessible tissue: Callus, score: 34.153 | N | N | N | N |
| vg1121803238 | A -> G | LOC_Os11g36950-LOC_Os11g36960 | intergenic_region ; MODIFIER | silent_mutation | Average:21.101; most accessible tissue: Callus, score: 34.153 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121803238 | NA | 1.16E-07 | mr1243 | 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 |
| vg1121803238 | NA | 1.60E-10 | mr1533 | 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 |
| vg1121803238 | 7.00E-07 | 6.44E-13 | mr1980 | 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 |
| vg1121803238 | NA | 8.85E-08 | mr1510_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 |
| vg1121803238 | NA | 1.48E-06 | mr1702_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 |