| Variant ID: vg0816229664 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16229664 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 78. )
CTCTCAAAAAGAGAGAAGGCAAAGTTTTGACTATCGCTGGGCACGATACTGTGATAGTTGGCTCAGGACGAGCAATTATTACACTCCCAATGGGTACACA[G/A,T]
ATTACAATCGAGGATGCTTTATTGTATCCGTCAAAATGGGTTTCACATTGAAACCCATATGCATTATCGAGAAGAATTTCTTCTCTTAACCAAACAAAAC
GTTTTGTTTGGTTAAGAGAAGAAATTCTTCTCGATAATGCATATGGGTTTCAATGTGAAACCCATTTTGACGGATACAATAAAGCATCCTCGATTGTAAT[C/T,A]
TGTGTACCCATTGGGAGTGTAATAATTGCTCGTCCTGAGCCAACTATCACAGTATCGTGCCCAGCGATAGTCAAAACTTTGCCTTCTCTCTTTTTGAGAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.80% | 37.00% | 2.71% | 5.29% | T: 0.19% |
| All Indica | 2759 | 81.10% | 16.50% | 2.17% | 0.00% | T: 0.25% |
| All Japonica | 1512 | 5.90% | 74.50% | 3.11% | 16.53% | NA |
| Aus | 269 | 84.40% | 9.70% | 5.20% | 0.00% | T: 0.74% |
| Indica I | 595 | 59.70% | 37.00% | 3.36% | 0.00% | NA |
| Indica II | 465 | 81.90% | 15.50% | 2.58% | 0.00% | NA |
| Indica III | 913 | 96.10% | 2.50% | 0.88% | 0.00% | T: 0.55% |
| Indica Intermediate | 786 | 79.50% | 17.70% | 2.54% | 0.00% | T: 0.25% |
| Temperate Japonica | 767 | 0.40% | 98.60% | 0.13% | 0.91% | NA |
| Tropical Japonica | 504 | 13.70% | 37.30% | 6.94% | 42.06% | NA |
| Japonica Intermediate | 241 | 7.10% | 75.50% | 4.56% | 12.86% | NA |
| VI/Aromatic | 96 | 4.20% | 92.70% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 58.90% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816229664 | G -> T | LOC_Os08g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.0; most accessible tissue: Callus, score: 24.819 | N | N | N | N |
| vg0816229664 | G -> A | LOC_Os08g26690.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.0; most accessible tissue: Callus, score: 24.819 | N | N | N | N |
| vg0816229664 | G -> DEL | N | N | silent_mutation | Average:12.0; most accessible tissue: Callus, score: 24.819 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816229664 | NA | 5.48E-09 | mr1575 | 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 |
| vg0816229664 | NA | 3.22E-06 | mr1646 | 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 |
| vg0816229664 | NA | 1.10E-09 | mr1714 | 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 |
| vg0816229664 | 4.43E-06 | 4.43E-06 | mr1918 | 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 |
| vg0816229664 | NA | 8.77E-06 | mr1911_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 |