| Variant ID: vg0320508322 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 20508322 |
| Reference Allele: A | Alternative Allele: G,AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.65, A: 0.33, others allele: 0.00, population size: 72. )
ATGTCAGCATCAGTGATTTTCTCTCCACATAGCTTAAGACAAGTGACAATGCGGTGAAGAACTGAGTTATATTACTCCACAGATTTGTAATCCTGGAAAC[A/G,AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG]
TAAGTGAAGCCACTCACGTTTTGCTTTTGGGAGCAAAGCCTTTACTTGATGGCCATAGCGATCCTTCAGTGAGTCCCAAAGGACCTTCGGATCTTCCTCA
TGAGGAAGATCCGAAGGTCCTTTGGGACTCACTGAAGGATCGCTATGGCCATCAAGTAAAGGCTTTGCTCCCAAAAGCAAAACGTGAGTGGCTTCACTTA[T/C,CGTTTCCAGGATTACAAATCTGTGGGTGGCTTCACTT]
GTTTCCAGGATTACAAATCTGTGGAGTAATATAACTCAGTTCTTCACCGCATTGTCACTTGTCTTAAGCTATGTGGAGAGAAAATCACTGATGCTGACAT
| 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 | 66.60% | 32.70% | 0.66% | 0.00% | AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG: 0.06% |
| All Indica | 2759 | 97.10% | 2.80% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 11.00% | 86.90% | 1.92% | 0.00% | AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG: 0.20% |
| Aus | 269 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.30% | 4.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 28.40% | 68.30% | 3.17% | 0.00% | AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG: 0.20% |
| Japonica Intermediate | 241 | 8.70% | 85.10% | 5.39% | 0.00% | AAGTGAAGCCACCCACAGATTTGTAATCCTGGAAACG: 0.83% |
| VI/Aromatic | 96 | 24.00% | 76.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 54.40% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320508322 | A -> AAGTGAAGCCACCCACAGATTTGTAATCCT GGAAACG | LOC_Os03g36970.1 | upstream_gene_variant ; 4129.0bp to feature; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0320508322 | A -> AAGTGAAGCCACCCACAGATTTGTAATCCT GGAAACG | LOC_Os03g37000.1 | upstream_gene_variant ; 3184.0bp to feature; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0320508322 | A -> AAGTGAAGCCACCCACAGATTTGTAATCCT GGAAACG | LOC_Os03g36980.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0320508322 | A -> G | LOC_Os03g36970.1 | upstream_gene_variant ; 4128.0bp to feature; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0320508322 | A -> G | LOC_Os03g37000.1 | upstream_gene_variant ; 3185.0bp to feature; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0320508322 | A -> G | LOC_Os03g36980.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.789; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0320508322 | NA | 4.92E-07 | mr1227 | 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 |
| vg0320508322 | NA | 8.01E-18 | mr1304 | 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 |
| vg0320508322 | NA | 7.96E-06 | mr1304 | 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 |
| vg0320508322 | NA | 1.70E-09 | mr1718 | 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 |
| vg0320508322 | NA | 1.11E-13 | mr1750 | 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 |
| vg0320508322 | NA | 9.06E-07 | mr1785 | 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 |
| vg0320508322 | NA | 5.08E-06 | mr1830 | 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 |
| vg0320508322 | NA | 5.54E-07 | mr1077_2 | 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 |
| vg0320508322 | NA | 4.99E-12 | mr1718_2 | 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 |
| vg0320508322 | 5.77E-06 | 1.21E-20 | mr1750_2 | 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 |
| vg0320508322 | 3.38E-06 | 5.68E-10 | mr1987_2 | 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 |