| Variant ID: vg0804698573 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4698573 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.05, others allele: 0.00, population size: 209. )
CCGGCGCAATTTATTTTAATTAGCTGGTTGATTCGGCGATTTCTTAGTGCAATTTCTGGGTCCAAATTACTTGCTTGATACACATGCATGCTGTTATTGC[A/G]
TCATTCACCACTCTCCCTAGCCAAACTGGAATTGCATAAGTTTCACAAATGTCTGATATGTAATGTTAAGTTTTAGATATTTGGCCAGATAGGTAGATAA
TTATCTACCTATCTGGCCAAATATCTAAAACTTAACATTACATATCAGACATTTGTGAAACTTATGCAATTCCAGTTTGGCTAGGGAGAGTGGTGAATGA[T/C]
GCAATAACAGCATGCATGTGTATCAAGCAAGTAATTTGGACCCAGAAATTGCACTAAGAAATCGCCGAATCAACCAGCTAATTAAAATAAATTGCGCCGG
| 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 | 58.50% | 41.40% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 89.10% | 10.80% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 12.20% | 87.60% | 0.13% | 0.00% | NA |
| Aus | 269 | 24.20% | 75.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 90.30% | 9.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.80% | 14.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 84.70% | 15.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 9.10% | 90.70% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 14.30% | 85.50% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 17.80% | 82.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 43.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804698573 | A -> G | LOC_Os08g08220.1 | upstream_gene_variant ; 2089.0bp to feature; MODIFIER | silent_mutation | Average:57.19; most accessible tissue: Callus, score: 79.361 | N | N | N | N |
| vg0804698573 | A -> G | LOC_Os08g08220.3 | upstream_gene_variant ; 2089.0bp to feature; MODIFIER | silent_mutation | Average:57.19; most accessible tissue: Callus, score: 79.361 | N | N | N | N |
| vg0804698573 | A -> G | LOC_Os08g08220.2 | upstream_gene_variant ; 2453.0bp to feature; MODIFIER | silent_mutation | Average:57.19; most accessible tissue: Callus, score: 79.361 | N | N | N | N |
| vg0804698573 | A -> G | LOC_Os08g08210.1 | downstream_gene_variant ; 1843.0bp to feature; MODIFIER | silent_mutation | Average:57.19; most accessible tissue: Callus, score: 79.361 | N | N | N | N |
| vg0804698573 | A -> G | LOC_Os08g08210-LOC_Os08g08220 | intergenic_region ; MODIFIER | silent_mutation | Average:57.19; most accessible tissue: Callus, score: 79.361 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804698573 | NA | 3.78E-27 | mr1037 | 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 |
| vg0804698573 | NA | 5.60E-09 | mr1610 | 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 |
| vg0804698573 | NA | 1.41E-12 | mr1914 | 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 |
| vg0804698573 | NA | 8.27E-34 | mr1037_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 |
| vg0804698573 | NA | 4.09E-19 | mr1131_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 |
| vg0804698573 | NA | 1.42E-18 | mr1199_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 |
| vg0804698573 | 1.41E-06 | 1.32E-07 | mr1671_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 |
| vg0804698573 | 2.30E-06 | 9.99E-50 | mr1721_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 |
| vg0804698573 | 7.65E-06 | NA | mr1721_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 |
| vg0804698573 | NA | 7.90E-12 | mr1782_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 |
| vg0804698573 | NA | 1.51E-14 | mr1938_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 |