| Variant ID: vg0828429675 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 28429675 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 227. )
ACGAGGTGGTTAGTATAGGCATGGCACATAGGACGTTAGGGTGGATAGCTTAGACGATGTCGGTGTCAAGCGAGTCGACTAACCGTACCGTTAAGGTAGG[C/T]
TGGCGGGCGCGACACTGTCGAAGGCAGATGGAGAATTCTGTGCGAAATTAAAACCTTGATAACTTTGCCTTTCGCTCATGGAATCGAGCTAGGTTTTTTT
AAAAAAACCTAGCTCGATTCCATGAGCGAAAGGCAAAGTTATCAAGGTTTTAATTTCGCACAGAATTCTCCATCTGCCTTCGACAGTGTCGCGCCCGCCA[G/A]
CCTACCTTAACGGTACGGTTAGTCGACTCGCTTGACACCGACATCGTCTAAGCTATCCACCCTAACGTCCTATGTGCCATGCCTATACTAACCACCTCGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.70% | 2.00% | 6.24% | 29.07% | NA |
| All Indica | 2759 | 44.00% | 0.00% | 8.26% | 47.77% | NA |
| All Japonica | 1512 | 87.20% | 6.20% | 4.30% | 2.31% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 49.40% | 0.00% | 16.30% | 34.29% | NA |
| Indica II | 465 | 46.90% | 0.00% | 6.24% | 46.88% | NA |
| Indica III | 913 | 36.10% | 0.00% | 4.49% | 59.36% | NA |
| Indica Intermediate | 786 | 47.20% | 0.00% | 7.76% | 45.04% | NA |
| Temperate Japonica | 767 | 80.60% | 11.50% | 6.00% | 1.96% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 0.99% | 1.39% | NA |
| Japonica Intermediate | 241 | 86.70% | 2.10% | 5.81% | 5.39% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 1.10% | 2.22% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0828429675 | C -> T | LOC_Os08g45260.1 | downstream_gene_variant ; 1173.0bp to feature; MODIFIER | silent_mutation | Average:32.571; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| vg0828429675 | C -> T | LOC_Os08g45240-LOC_Os08g45260 | intergenic_region ; MODIFIER | silent_mutation | Average:32.571; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| vg0828429675 | C -> DEL | N | N | silent_mutation | Average:32.571; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0828429675 | 2.23E-06 | NA | mr1044 | 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 |
| vg0828429675 | NA | 1.08E-06 | mr1045 | 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 |
| vg0828429675 | NA | 6.11E-07 | mr1617 | 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 |
| vg0828429675 | NA | 9.21E-08 | mr1570_2 | 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 |
| vg0828429675 | NA | 6.08E-06 | mr1617_2 | 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 |