| Variant ID: vg0812970658 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 12970658 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 88. )
GCGAAGTGAGTTTTTGCCACGATTGCACCCAATACACTCGAATATGTCCAAAAATCATGTTTTGGTTCTTTTTGAAATTTTTCGTTCCGGTTAAAAACAA[A/C]
GCACCCACGAGTGGCAATATCGGCATTAATTGATAAAAGTTCGCTGCGCGAGTCGCGAAGTGAGTTTTTTCCACGAACGCACCCAATACGCTCCAATATG
CATATTGGAGCGTATTGGGTGCGTTCGTGGAAAAAACTCACTTCGCGACTCGCGCAGCGAACTTTTATCAATTAATGCCGATATTGCCACTCGTGGGTGC[T/G]
TTGTTTTTAACCGGAACGAAAAATTTCAAAAAGAACCAAAACATGATTTTTGGACATATTCGAGTGTATTGGGTGCAATCGTGGCAAAAACTCACTTCGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.80% | 6.70% | 20.50% | 53.00% | NA |
| All Indica | 2759 | 10.50% | 1.30% | 18.52% | 69.70% | NA |
| All Japonica | 1512 | 37.20% | 16.70% | 17.46% | 28.64% | NA |
| Aus | 269 | 24.50% | 6.30% | 57.62% | 11.52% | NA |
| Indica I | 595 | 3.20% | 1.50% | 18.82% | 76.47% | NA |
| Indica II | 465 | 5.40% | 2.20% | 15.05% | 77.42% | NA |
| Indica III | 913 | 18.10% | 0.90% | 16.43% | 64.62% | NA |
| Indica Intermediate | 786 | 10.20% | 1.10% | 22.77% | 65.90% | NA |
| Temperate Japonica | 767 | 44.70% | 30.20% | 20.47% | 4.56% | NA |
| Tropical Japonica | 504 | 30.60% | 1.60% | 12.90% | 54.96% | NA |
| Japonica Intermediate | 241 | 27.00% | 5.40% | 17.43% | 50.21% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 13.54% | 80.21% | NA |
| Intermediate | 90 | 12.20% | 13.30% | 28.89% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0812970658 | A -> C | LOC_Os08g21695.1 | downstream_gene_variant ; 371.0bp to feature; MODIFIER | silent_mutation | Average:23.487; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0812970658 | A -> C | LOC_Os08g21690-LOC_Os08g21695 | intergenic_region ; MODIFIER | silent_mutation | Average:23.487; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0812970658 | A -> DEL | N | N | silent_mutation | Average:23.487; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0812970658 | 1.32E-06 | NA | mr1486_2 | 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 |
| vg0812970658 | NA | 3.45E-06 | mr1577_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 |
| vg0812970658 | 8.17E-06 | NA | mr1588_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 |
| vg0812970658 | 8.26E-06 | NA | mr1768_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 |
| vg0812970658 | NA | 3.77E-06 | mr1768_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 |
| vg0812970658 | 5.92E-06 | 5.89E-06 | mr1919_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 |