| Variant ID: vg0906303350 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6303350 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, C: 0.20, others allele: 0.00, population size: 69. )
AAGCGGAAGCGTAATTAATTAATTTATTACATGGGCGGCGAAGACCCAATACACAAGAAGACAAACGAAAAACAGCGGAAGACTAGGGTGTCGACCACAT[C/G]
CGCTTGACGGCAGGCACGAGCCAGACACCAAAGCCTTCATCATCCAGGGGCTCCTCTTCTGGGTTTGGCAAAAATTGAGAAAGACTGAGTACAACCACCG
CGGTGGTTGTACTCAGTCTTTCTCAATTTTTGCCAAACCCAGAAGAGGAGCCCCTGGATGATGAAGGCTTTGGTGTCTGGCTCGTGCCTGCCGTCAAGCG[G/C]
ATGTGGTCGACACCCTAGTCTTCCGCTGTTTTTCGTTTGTCTTCTTGTGTATTGGGTCTTCGCCGCCCATGTAATAAATTAATTAATTACGCTTCCGCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 9.30% | 1.88% | 55.86% | NA |
| All Indica | 2759 | 9.70% | 7.00% | 2.25% | 81.04% | NA |
| All Japonica | 1512 | 81.60% | 14.40% | 0.00% | 3.97% | NA |
| Aus | 269 | 2.20% | 6.30% | 8.55% | 82.90% | NA |
| Indica I | 595 | 15.80% | 9.20% | 1.01% | 73.95% | NA |
| Indica II | 465 | 9.00% | 0.20% | 5.59% | 85.16% | NA |
| Indica III | 913 | 7.40% | 5.70% | 1.97% | 84.88% | NA |
| Indica Intermediate | 786 | 8.00% | 10.90% | 1.53% | 79.52% | NA |
| Temperate Japonica | 767 | 92.60% | 6.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 82.70% | 15.50% | 0.00% | 1.79% | NA |
| Japonica Intermediate | 241 | 44.40% | 39.00% | 0.00% | 16.60% | NA |
| VI/Aromatic | 96 | 8.30% | 3.10% | 0.00% | 88.54% | NA |
| Intermediate | 90 | 46.70% | 8.90% | 4.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906303350 | C -> G | LOC_Os09g11350.1 | downstream_gene_variant ; 1155.0bp to feature; MODIFIER | silent_mutation | Average:36.812; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0906303350 | C -> G | LOC_Os09g11360.1 | downstream_gene_variant ; 2258.0bp to feature; MODIFIER | silent_mutation | Average:36.812; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0906303350 | C -> G | LOC_Os09g11350-LOC_Os09g11360 | intergenic_region ; MODIFIER | silent_mutation | Average:36.812; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| vg0906303350 | C -> DEL | N | N | silent_mutation | Average:36.812; most accessible tissue: Minghui63 young leaf, score: 62.741 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906303350 | NA | 6.64E-06 | mr1768_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 |
| vg0906303350 | NA | 4.84E-07 | mr1805_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 |
| vg0906303350 | 5.65E-06 | 1.87E-08 | mr1842_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 |