| Variant ID: vg0716180373 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16180373 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )
TTATAATAGGATTCATAGCCGATGCCGGCGCTCTCTGCATCGCTCCAAACTTCTGACAATCTTGACAACCTTTATAATATCTGAAACAATCCTCGAGCAT[C/T]
GTCAGCAAAAAATACCCGGCACGTCGAAGCAACCACTTCATTTTATGAGCCGACTGATGAGTGCCACATAACTTCGCCGATTGCAACTTTTGCCTAATCG
CGATTAGGCAAAAGTTGCAATCGGCGAAGTTATGTGGCACTCATCAGTCGGCTCATAAAATGAAGTGGTTGCTTCGACGTGCCGGGTATTTTTTGCTGAC[G/A]
ATGCTCGAGGATTGTTTCAGATATTATAAAGGTTGTCAAGATTGTCAGAAGTTTGGAGCGATGCAGAGAGCGCCGGCATCGGCTATGAATCCTATTATAA
| 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 | 64.10% | 8.10% | 22.85% | 4.95% | NA |
| All Indica | 2759 | 42.20% | 13.30% | 36.17% | 8.37% | NA |
| All Japonica | 1512 | 99.50% | 0.20% | 0.26% | 0.07% | NA |
| Aus | 269 | 77.00% | 3.70% | 19.33% | 0.00% | NA |
| Indica I | 595 | 49.70% | 11.60% | 22.35% | 16.30% | NA |
| Indica II | 465 | 45.40% | 7.50% | 39.14% | 7.96% | NA |
| Indica III | 913 | 29.70% | 17.30% | 47.43% | 5.59% | NA |
| Indica Intermediate | 786 | 49.10% | 13.20% | 31.81% | 5.85% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 4.40% | 25.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0716180373 | C -> DEL | N | N | silent_mutation | Average:24.845; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0716180373 | C -> T | LOC_Os07g27730.1 | downstream_gene_variant ; 1331.0bp to feature; MODIFIER | silent_mutation | Average:24.845; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0716180373 | C -> T | LOC_Os07g27740.1 | intron_variant ; MODIFIER | silent_mutation | Average:24.845; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716180373 | NA | 9.87E-06 | mr1524_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 |
| vg0716180373 | NA | 3.81E-06 | mr1746_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 |
| vg0716180373 | 7.92E-06 | 7.89E-06 | mr1760_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 |
| vg0716180373 | 2.45E-06 | NA | mr1950_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 |