| Variant ID: vg0622289516 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 22289516 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 127. )
AATTAGCAGTTTCTACCGCACGTTTTTTTTCAGACTATTTAACAGTACGTTTTGTGCAAAAAATTTATATATAAAAGTTGCTTTAAAATACAAATATATT[C/T]
ATTTTCAAGTTTATAATAATTAAAACTAATTAATTATTTACTACTACATCCGTCCTATATAAATTGCACTTCTATCTAATTTAGGACAAAATAGTAGGAT
ATCCTACTATTTTGTCCTAAATTAGATAGAAGTGCAATTTATATAGGACGGATGTAGTAGTAAATAATTAATTAGTTTTAATTATTATAAACTTGAAAAT[G/A]
AATATATTTGTATTTTAAAGCAACTTTTATATATAAATTTTTTGCACAAAACGTACTGTTAAATAGTCTGAAAAAAAACGTGCGGTAGAAACTGCTAATT
| 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 | 32.20% | 4.70% | 12.21% | 50.85% | NA |
| All Indica | 2759 | 6.10% | 1.40% | 17.47% | 75.03% | NA |
| All Japonica | 1512 | 85.10% | 0.10% | 0.79% | 14.09% | NA |
| Aus | 269 | 14.90% | 56.10% | 4.46% | 24.54% | NA |
| Indica I | 595 | 2.70% | 0.20% | 11.76% | 85.38% | NA |
| Indica II | 465 | 4.70% | 1.10% | 12.69% | 81.51% | NA |
| Indica III | 913 | 8.10% | 2.30% | 27.27% | 62.32% | NA |
| Indica Intermediate | 786 | 7.10% | 1.50% | 13.23% | 78.12% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.78% | 1.69% | NA |
| Tropical Japonica | 504 | 63.70% | 0.20% | 0.40% | 35.71% | NA |
| Japonica Intermediate | 241 | 90.00% | 0.00% | 1.66% | 8.30% | NA |
| VI/Aromatic | 96 | 8.30% | 31.20% | 54.17% | 6.25% | NA |
| Intermediate | 90 | 24.40% | 1.10% | 21.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0622289516 | C -> T | LOC_Os06g37630.1 | upstream_gene_variant ; 3022.0bp to feature; MODIFIER | silent_mutation | Average:45.686; most accessible tissue: Callus, score: 89.477 | N | N | N | N |
| vg0622289516 | C -> T | LOC_Os06g37640.1 | downstream_gene_variant ; 2730.0bp to feature; MODIFIER | silent_mutation | Average:45.686; most accessible tissue: Callus, score: 89.477 | N | N | N | N |
| vg0622289516 | C -> T | LOC_Os06g37630-LOC_Os06g37640 | intergenic_region ; MODIFIER | silent_mutation | Average:45.686; most accessible tissue: Callus, score: 89.477 | N | N | N | N |
| vg0622289516 | C -> DEL | N | N | silent_mutation | Average:45.686; most accessible tissue: Callus, score: 89.477 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0622289516 | NA | 3.76E-06 | mr1633 | 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 |
| vg0622289516 | 3.30E-06 | NA | mr1141_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 |
| vg0622289516 | NA | 3.82E-06 | mr1341_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 |
| vg0622289516 | NA | 2.74E-08 | mr1347_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 |
| vg0622289516 | NA | 8.55E-07 | mr1406_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 |