| Variant ID: vg0909036511 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9036511 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGCCCAGTTTCTCCTGGTCGATTGCCATGACTTCCGAGCTGTCCATGGGCACACTTGGAGCATGTAGGACTTCGAAAAAGATGCCAGGCGAATATGGGCC[A/G]
CCACAAGCAACGGATTTCGCCAAGGCGTCTACTTCCTCGTTCTGGTCTCTAGGCAAGTGTTCGACCGTTATGCCGGTGAAGCATTTTTCATGGATCGAAT
ATTCGATCCATGAAAAATGCTTCACCGGCATAACGGTCGAACACTTGCCTAGAGACCAGAACGAGGAAGTAGACGCCTTGGCGAAATCCGTTGCTTGTGG[T/C]
GGCCCATATTCGCCTGGCATCTTTTTCGAAGTCCTACATGCTCCAAGTGTGCCCATGGACAGCTCGGAAGTCATGGCAATCGACCAGGAGAAACTGGGCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.30% | 38.20% | 16.40% | 4.08% | NA |
| All Indica | 2759 | 11.90% | 59.30% | 24.68% | 4.06% | NA |
| All Japonica | 1512 | 90.20% | 7.70% | 0.60% | 1.46% | NA |
| Aus | 269 | 56.90% | 12.60% | 29.74% | 0.74% | NA |
| Indica I | 595 | 8.20% | 66.90% | 21.01% | 3.87% | NA |
| Indica II | 465 | 7.30% | 64.90% | 20.22% | 7.53% | NA |
| Indica III | 913 | 15.90% | 51.50% | 28.92% | 3.72% | NA |
| Indica Intermediate | 786 | 12.80% | 59.40% | 25.19% | 2.54% | NA |
| Temperate Japonica | 767 | 93.90% | 5.70% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 93.30% | 3.00% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 72.20% | 24.10% | 2.07% | 1.66% | NA |
| VI/Aromatic | 96 | 44.80% | 2.10% | 2.08% | 51.04% | NA |
| Intermediate | 90 | 70.00% | 17.80% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909036511 | A -> G | LOC_Os09g15000.1 | downstream_gene_variant ; 1798.0bp to feature; MODIFIER | silent_mutation | Average:34.448; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| vg0909036511 | A -> G | LOC_Os09g15010.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.448; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| vg0909036511 | A -> DEL | N | N | silent_mutation | Average:34.448; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909036511 | NA | 7.17E-06 | mr1280 | 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 |
| vg0909036511 | NA | 6.82E-06 | mr1318 | 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 |
| vg0909036511 | 9.41E-07 | NA | mr1689 | 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 |