| Variant ID: vg0402387202 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2387202 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )
GACTGGCAGCTTGTGGCCATAGTCGACAACAATCCAAGAAGAGAAGACCTGGTACATCCAGGAGCACATGATGTCAAAAGCAATAGAATCTTCATCTTCT[C/T]
GTTTGGGTTTAGTCTAGCCCTCATACTTGAAGGTTGGCTTTGATCTCTCCTTGATTGGGGTCAGCCGACACTTTATAAGATGTCGAGTGACTTGTTCCCC
GGGGAACAAGTCACTCGACATCTTATAAAGTGTCGGCTGACCCCAATCAAGGAGAGATCAAAGCCAACCTTCAAGTATGAGGGCTAGACTAAACCCAAAC[G/A]
AGAAGATGAAGATTCTATTGCTTTTGACATCATGTGCTCCTGGATGTACCAGGTCTTCTCTTCTTGGATTGTTGTCGACTATGGCCACAAGCTGCCAGTC
| 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 | 90.40% | 4.50% | 4.02% | 1.02% | NA |
| All Indica | 2759 | 84.50% | 7.40% | 6.42% | 1.74% | NA |
| All Japonica | 1512 | 99.40% | 0.20% | 0.40% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 57.10% | 22.40% | 20.34% | 0.17% | NA |
| Indica II | 465 | 90.10% | 3.70% | 6.24% | 0.00% | NA |
| Indica III | 913 | 95.80% | 0.00% | 0.44% | 3.72% | NA |
| Indica Intermediate | 786 | 88.50% | 6.90% | 2.93% | 1.65% | NA |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 4.40% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402387202 | C -> DEL | N | N | silent_mutation | Average:40.679; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |
| vg0402387202 | C -> T | LOC_Os04g04940.1 | upstream_gene_variant ; 3037.0bp to feature; MODIFIER | silent_mutation | Average:40.679; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |
| vg0402387202 | C -> T | LOC_Os04g04950.1 | downstream_gene_variant ; 3076.0bp to feature; MODIFIER | silent_mutation | Average:40.679; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |
| vg0402387202 | C -> T | LOC_Os04g04940-LOC_Os04g04950 | intergenic_region ; MODIFIER | silent_mutation | Average:40.679; most accessible tissue: Minghui63 young leaf, score: 66.656 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402387202 | NA | 4.39E-06 | mr1182 | 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 |
| vg0402387202 | NA | 5.58E-06 | mr1274 | 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 |
| vg0402387202 | 8.08E-06 | NA | mr1565 | 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 |
| vg0402387202 | 3.77E-06 | 6.87E-09 | mr1565 | 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 |