| Variant ID: vg1117144922 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17144922 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, G: 0.45, others allele: 0.00, population size: 73. )
CACAACGCGATCCTGGAAGAAAAAGATAAAAGGGTCGTTGAGTACACTCACGTTGATTGCAGCTTCGCGTTCGGCCGTCCCCTCCTCGCAAAGGGGGACG[A/G]
CGATGTTGCTCGCCGTTGTGGGGCCGCTGATCATTACTTGACCGACGCAGCGCTCCACAGTTTCGCTGTTCAAACCTGTAGGATCGAGAAGCAGAACTCG
CGAGTTCTGCTTCTCGATCCTACAGGTTTGAACAGCGAAACTGTGGAGCGCTGCGTCGGTCAAGTAATGATCAGCGGCCCCACAACGGCGAGCAACATCG[T/C]
CGTCCCCCTTTGCGAGGAGGGGACGGCCGAACGCGAAGCTGCAATCAACGTGAGTGTACTCAACGACCCTTTTATCTTTTTCTTCCAGGATCGCGTTGTG
| 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 | 48.20% | 19.10% | 0.99% | 31.70% | NA |
| All Indica | 2759 | 71.20% | 5.60% | 0.65% | 22.58% | NA |
| All Japonica | 1512 | 13.00% | 46.80% | 1.19% | 38.96% | NA |
| Aus | 269 | 23.80% | 8.20% | 0.74% | 67.29% | NA |
| Indica I | 595 | 88.60% | 4.00% | 1.18% | 6.22% | NA |
| Indica II | 465 | 46.50% | 14.40% | 0.86% | 38.28% | NA |
| Indica III | 913 | 75.90% | 0.20% | 0.11% | 23.77% | NA |
| Indica Intermediate | 786 | 67.20% | 7.80% | 0.76% | 24.30% | NA |
| Temperate Japonica | 767 | 2.20% | 84.60% | 0.52% | 12.65% | NA |
| Tropical Japonica | 504 | 30.20% | 3.40% | 1.98% | 64.48% | NA |
| Japonica Intermediate | 241 | 11.60% | 17.40% | 1.66% | 69.29% | NA |
| VI/Aromatic | 96 | 8.30% | 1.00% | 6.25% | 84.38% | NA |
| Intermediate | 90 | 52.20% | 17.80% | 3.33% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117144922 | A -> DEL | N | N | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1117144922 | A -> G | LOC_Os11g29540.1 | upstream_gene_variant ; 707.0bp to feature; MODIFIER | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1117144922 | A -> G | LOC_Os11g29550.1 | upstream_gene_variant ; 246.0bp to feature; MODIFIER | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1117144922 | A -> G | LOC_Os11g29560.1 | upstream_gene_variant ; 4697.0bp to feature; MODIFIER | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1117144922 | A -> G | LOC_Os11g29530.1 | downstream_gene_variant ; 3048.0bp to feature; MODIFIER | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| vg1117144922 | A -> G | LOC_Os11g29540-LOC_Os11g29550 | intergenic_region ; MODIFIER | silent_mutation | Average:55.831; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117144922 | NA | 1.24E-07 | mr1190 | 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 |
| vg1117144922 | 2.88E-06 | 2.88E-06 | mr1050_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 |
| vg1117144922 | NA | 3.51E-06 | mr1957_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 |