| Variant ID: vg0303412434 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 3412434 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, G: 0.43, others allele: 0.00, population size: 86. )
TCCCATACAAGTTTTGGAGGAATTTTAACAAGAGGTAGAACCTCATGGAAGAAATCCTTTGAGTCTTTATCTCTCCTCAAATTCCTATGTTTTTCCTGTG[A/G]
TCCAATCAAACGGTCATTTCTATGTTTTTCCTGTGTTTTGTAATCCTCTGTTTTACACTTACATTCCTGTCAGAATCTTATGTTTTTTCTATTCCTCCGT
ACGGAGGAATAGAAAAAACATAAGATTCTGACAGGAATGTAAGTGTAAAACAGAGGATTACAAAACACAGGAAAAACATAGAAATGACCGTTTGATTGGA[T/C]
CACAGGAAAAACATAGGAATTTGAGGAGAGATAAAGACTCAAAGGATTTCTTCCATGAGGTTCTACCTCTTGTTAAAATTCCTCCAAAACTTGTATGGGA
| 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 | 55.40% | 31.40% | 5.06% | 8.21% | NA |
| All Indica | 2759 | 76.00% | 3.80% | 7.18% | 13.05% | NA |
| All Japonica | 1512 | 21.90% | 76.10% | 1.06% | 0.93% | NA |
| Aus | 269 | 36.10% | 54.30% | 5.95% | 3.72% | NA |
| Indica I | 595 | 85.90% | 3.00% | 5.71% | 5.38% | NA |
| Indica II | 465 | 70.50% | 6.50% | 10.11% | 12.90% | NA |
| Indica III | 913 | 72.30% | 1.80% | 6.57% | 19.39% | NA |
| Indica Intermediate | 786 | 76.10% | 5.10% | 7.25% | 11.58% | NA |
| Temperate Japonica | 767 | 17.90% | 80.60% | 1.17% | 0.39% | NA |
| Tropical Japonica | 504 | 15.70% | 82.70% | 0.60% | 0.99% | NA |
| Japonica Intermediate | 241 | 47.70% | 48.10% | 1.66% | 2.49% | NA |
| VI/Aromatic | 96 | 53.10% | 44.80% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 45.60% | 42.20% | 8.89% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0303412434 | A -> DEL | N | N | silent_mutation | Average:44.392; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0303412434 | A -> G | LOC_Os03g06720.1 | upstream_gene_variant ; 4890.0bp to feature; MODIFIER | silent_mutation | Average:44.392; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0303412434 | A -> G | LOC_Os03g06710.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.392; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0303412434 | NA | 3.82E-11 | Plant_height | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0303412434 | 1.01E-07 | NA | mr1118 | 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 |
| vg0303412434 | NA | 9.19E-06 | mr1180 | 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 |
| vg0303412434 | NA | 9.61E-06 | mr1441 | 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 |
| vg0303412434 | NA | 3.62E-06 | mr1164_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 |
| vg0303412434 | NA | 2.03E-06 | mr1221_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 |