| Variant ID: vg0812030698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 12030698 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 104. )
TTGGAGAAATCTTTTATGAAGCGCCTATAGAACCCCACGTGACCCAAGAAGCTACGGACTCCCTTGACATTGACAGGAGGTGGAAGCTGTCAAATTACTT[T/C]
GATTTTTGCTCTGTCCACCTCAATTCCCCTTTCGGAGATTTGATATCCCAGGACTATTCCTTCACGAACCATGAAGTGGCACTTTTCCCAATTAAGTACC
GGTACTTAATTGGGAAAAGTGCCACTTCATGGTTCGTGAAGGAATAGTCCTGGGATATCAAATCTCCGAAAGGGGAATTGAGGTGGACAGAGCAAAAATC[A/G]
AAGTAATTTGACAGCTTCCACCTCCTGTCAATGTCAAGGGAGTCCGTAGCTTCTTGGGTCACGTGGGGTTCTATAGGCGCTTCATAAAAGATTTCTCCAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.80% | 7.40% | 5.27% | 54.49% | NA |
| All Indica | 2759 | 5.10% | 9.60% | 6.02% | 79.30% | NA |
| All Japonica | 1512 | 84.20% | 4.80% | 4.70% | 6.35% | NA |
| Aus | 269 | 1.50% | 0.70% | 2.60% | 95.17% | NA |
| Indica I | 595 | 7.10% | 2.40% | 1.01% | 89.58% | NA |
| Indica II | 465 | 8.60% | 4.90% | 2.15% | 84.30% | NA |
| Indica III | 913 | 1.10% | 17.40% | 11.94% | 69.55% | NA |
| Indica Intermediate | 786 | 6.10% | 8.80% | 5.22% | 79.90% | NA |
| Temperate Japonica | 767 | 95.30% | 0.30% | 1.69% | 2.74% | NA |
| Tropical Japonica | 504 | 67.90% | 12.30% | 10.12% | 9.72% | NA |
| Japonica Intermediate | 241 | 83.00% | 3.30% | 2.90% | 10.79% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 2.08% | 4.17% | NA |
| Intermediate | 90 | 55.60% | 6.70% | 3.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0812030698 | T -> C | LOC_Os08g20070.1 | downstream_gene_variant ; 2997.0bp to feature; MODIFIER | silent_mutation | Average:10.99; most accessible tissue: Callus, score: 33.6 | N | N | N | N |
| vg0812030698 | T -> C | LOC_Os08g20060.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.99; most accessible tissue: Callus, score: 33.6 | N | N | N | N |
| vg0812030698 | T -> DEL | N | N | silent_mutation | Average:10.99; most accessible tissue: Callus, score: 33.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0812030698 | 1.11E-06 | 1.97E-08 | mr1134 | 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 |
| vg0812030698 | NA | 8.65E-06 | mr1135 | 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 |
| vg0812030698 | NA | 6.19E-07 | mr1504 | 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 |
| vg0812030698 | NA | 1.69E-06 | mr1510 | 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 |
| vg0812030698 | NA | 3.87E-06 | mr1695 | 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 |
| vg0812030698 | NA | 2.59E-08 | mr1600_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 |