| Variant ID: vg0329971617 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29971617 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 82. )
TCTGTATTCCTTCACGCACAGATCCACCAGAACACAGGAGTAGGGTGTTACGCTTCTCAGCGGTCCGAACCTGTCTACGTCGCCCGTGTCTTGTGCATTT[T/C]
CTCTCTCGCTGACGTTCCTCAGATCGAGGGCGAAGAACCTCACTTAGCGCCCCCGGCCGAACCGGCAAAGGGGGGCCTGCGCGGTCTCCCGGTGAGGAGC
GCTCCTCACCGGGAGACCGCGCAGGCCCCCCTTTGCCGGTTCGGCCGGGGGCGCTAAGTGAGGTTCTTCGCCCTCGATCTGAGGAACGTCAGCGAGAGAG[A/G]
AAATGCACAAGACACGGGCGACGTAGACAGGTTCGGACCGCTGAGAAGCGTAACACCCTACTCCTGTGTTCTGGTGGATCTGTGCGTGAAGGAATACAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 28.20% | 7.20% | 4.91% | 59.65% | NA |
| All Indica | 2759 | 2.20% | 0.40% | 5.73% | 91.70% | NA |
| All Japonica | 1512 | 80.30% | 16.80% | 2.05% | 0.86% | NA |
| Aus | 269 | 3.00% | 0.00% | 12.64% | 84.39% | NA |
| Indica I | 595 | 1.00% | 0.00% | 2.18% | 96.81% | NA |
| Indica II | 465 | 3.40% | 0.90% | 2.37% | 93.33% | NA |
| Indica III | 913 | 1.80% | 0.10% | 10.19% | 87.95% | NA |
| Indica Intermediate | 786 | 2.90% | 0.60% | 5.22% | 91.22% | NA |
| Temperate Japonica | 767 | 88.90% | 8.60% | 1.83% | 0.65% | NA |
| Tropical Japonica | 504 | 79.80% | 16.90% | 2.38% | 0.99% | NA |
| Japonica Intermediate | 241 | 53.90% | 42.70% | 2.07% | 1.24% | NA |
| VI/Aromatic | 96 | 14.60% | 69.80% | 5.21% | 10.42% | NA |
| Intermediate | 90 | 42.20% | 10.00% | 4.44% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329971617 | T -> C | LOC_Os03g52200.1 | upstream_gene_variant ; 1673.0bp to feature; MODIFIER | silent_mutation | Average:13.063; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0329971617 | T -> C | LOC_Os03g52230.1 | downstream_gene_variant ; 4874.0bp to feature; MODIFIER | silent_mutation | Average:13.063; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0329971617 | T -> C | LOC_Os03g52210.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.063; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0329971617 | T -> DEL | N | N | silent_mutation | Average:13.063; 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 |
|---|---|---|---|---|---|---|
| vg0329971617 | NA | 5.89E-06 | mr1293 | 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 |
| vg0329971617 | NA | 7.84E-06 | mr1648 | 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 |
| vg0329971617 | NA | 8.18E-06 | mr1731 | 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 |