| Variant ID: vg0909165763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9165763 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCACTATTTCTAAGCATATTAGAGCCCGTCACAGATAGAAGGATCTGTACTAGTGTGAGGGCTGAGGATGGTGGTGGCGATGGACGGGAAGGAGATCTT[T/A]
TTTTTTTCCTTTCTATTACTTTTCATCAACCATGTTTGATTGTTGATTTTTTTTCATCCTCTTTTTTTTCTTTTCCTTGTTCTCTACATGGGCCCAGCTC
GAGCTGGGCCCATGTAGAGAACAAGGAAAAGAAAAAAAAGAGGATGAAAAAAAATCAACAATCAAACATGGTTGATGAAAAGTAATAGAAAGGAAAAAAA[A/T]
AAGATCTCCTTCCCGTCCATCGCCACCACCATCCTCAGCCCTCACACTAGTACAGATCCTTCTATCTGTGACGGGCTCTAATATGCTTAGAAATAGTGGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.00% | 30.00% | 11.26% | 12.74% | NA |
| All Indica | 2759 | 62.50% | 5.70% | 17.76% | 14.10% | NA |
| All Japonica | 1512 | 15.00% | 76.40% | 1.06% | 7.54% | NA |
| Aus | 269 | 67.70% | 16.40% | 5.58% | 10.41% | NA |
| Indica I | 595 | 54.50% | 6.10% | 30.92% | 8.57% | NA |
| Indica II | 465 | 58.90% | 1.30% | 20.65% | 19.14% | NA |
| Indica III | 913 | 66.60% | 7.10% | 8.76% | 17.52% | NA |
| Indica Intermediate | 786 | 65.90% | 6.20% | 16.54% | 11.32% | NA |
| Temperate Japonica | 767 | 12.60% | 74.10% | 1.56% | 11.73% | NA |
| Tropical Japonica | 504 | 11.50% | 84.50% | 0.40% | 3.57% | NA |
| Japonica Intermediate | 241 | 29.90% | 66.80% | 0.83% | 2.49% | NA |
| VI/Aromatic | 96 | 18.80% | 18.80% | 3.12% | 59.38% | NA |
| Intermediate | 90 | 24.40% | 51.10% | 8.89% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909165763 | T -> DEL | N | N | silent_mutation | Average:51.971; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
| vg0909165763 | T -> A | LOC_Os09g15100-LOC_Os09g15120 | intergenic_region ; MODIFIER | silent_mutation | Average:51.971; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909165763 | 5.60E-06 | NA | mr1692 | 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 |
| vg0909165763 | NA | 2.34E-10 | mr1705_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 |