| Variant ID: vg0806714162 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 6714162 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )
GCCTCGTCTGTTGCCGACCGGTCTACTCGCCCCCATGATTGGTGCACCCTGTAGCCGTTGCTGATGGCAACATCGTCTTCACCGCTGGTTCACCTTCGCC[G/A]
TTGCCGACTGGTGCCTTCACCTACACGGCGAGCCTATTATGGTGCCACTCATGGACGTCGACATTTTCACCATTATTCTGCTTCTTCCATCGCCGGCTGA
TCAGCCGGCGATGGAAGAAGCAGAATAATGGTGAAAATGTCGACGTCCATGAGTGGCACCATAATAGGCTCGCCGTGTAGGTGAAGGCACCAGTCGGCAA[C/T]
GGCGAAGGTGAACCAGCGGTGAAGACGATGTTGCCATCAGCAACGGCTACAGGGTGCACCAATCATGGGGGCGAGTAGACCGGTCGGCAACAGACGAGGC
| 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 | 92.00% | 2.30% | 2.22% | 3.51% | NA |
| All Indica | 2759 | 87.00% | 3.70% | 3.44% | 5.80% | NA |
| All Japonica | 1512 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Aus | 269 | 97.40% | 0.00% | 1.49% | 1.12% | NA |
| Indica I | 595 | 94.30% | 3.40% | 2.35% | 0.00% | NA |
| Indica II | 465 | 86.20% | 8.20% | 2.80% | 2.80% | NA |
| Indica III | 913 | 83.90% | 0.20% | 4.16% | 11.72% | NA |
| Indica Intermediate | 786 | 85.60% | 5.50% | 3.82% | 5.09% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 0.60% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0806714162 | G -> A | LOC_Os08g11440-LOC_Os08g11450 | intergenic_region ; MODIFIER | silent_mutation | Average:57.933; most accessible tissue: Zhenshan97 young leaf, score: 85.715 | N | N | N | N |
| vg0806714162 | G -> DEL | N | N | silent_mutation | Average:57.933; most accessible tissue: Zhenshan97 young leaf, score: 85.715 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0806714162 | 4.60E-06 | 5.62E-06 | mr1319 | 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 |
| vg0806714162 | 6.80E-06 | 6.80E-06 | mr1840 | 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 |