| Variant ID: vg0514453167 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 14453167 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTCCGATTTACATGTAAAAACTACTTTAAACCGATTTTTCTCTTAAATTACTTATCCAAATCATGATTCGATTGCATCATTAAATTTGTTGCAATTAAAT[T/C]
TTCAAAACAAGACCACACATGGATATATTCCGATGAATTTTTTTTAGCTTATTATTGAATTATTTTTAAATGTTGCACGATGTTCCACCAGGTATATCGG
CCGATATACCTGGTGGAACATCGTGCAACATTTAAAAATAATTCAATAATAAGCTAAAAAAAATTCATCGGAATATATCCATGTGTGGTCTTGTTTTGAA[A/G]
ATTTAATTGCAACAAATTTAATGATGCAATCGAATCATGATTTGGATAAGTAATTTAAGAGAAAAATCGGTTTAAAGTAGTTTTTACATGTAAATCGGAC
| 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 | 46.90% | 11.10% | 3.58% | 38.45% | NA |
| All Indica | 2759 | 19.20% | 13.80% | 5.15% | 61.83% | NA |
| All Japonica | 1512 | 97.50% | 0.80% | 0.00% | 1.72% | NA |
| Aus | 269 | 27.10% | 44.60% | 8.18% | 20.07% | NA |
| Indica I | 595 | 12.60% | 20.20% | 2.35% | 64.87% | NA |
| Indica II | 465 | 18.90% | 1.30% | 3.87% | 75.91% | NA |
| Indica III | 913 | 20.00% | 18.80% | 7.89% | 53.23% | NA |
| Indica Intermediate | 786 | 23.30% | 10.70% | 4.83% | 61.20% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 97.40% | 2.20% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 5.60% | 5.56% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0514453167 | T -> DEL | N | N | silent_mutation | Average:78.322; most accessible tissue: Minghui63 panicle, score: 94.794 | N | N | N | N |
| vg0514453167 | T -> C | LOC_Os05g24970.1 | upstream_gene_variant ; 984.0bp to feature; MODIFIER | silent_mutation | Average:78.322; most accessible tissue: Minghui63 panicle, score: 94.794 | N | N | N | N |
| vg0514453167 | T -> C | LOC_Os05g24970.2 | upstream_gene_variant ; 856.0bp to feature; MODIFIER | silent_mutation | Average:78.322; most accessible tissue: Minghui63 panicle, score: 94.794 | N | N | N | N |
| vg0514453167 | T -> C | LOC_Os05g24970.3 | upstream_gene_variant ; 856.0bp to feature; MODIFIER | silent_mutation | Average:78.322; most accessible tissue: Minghui63 panicle, score: 94.794 | N | N | N | N |
| vg0514453167 | T -> C | LOC_Os05g24970-LOC_Os05g24980 | intergenic_region ; MODIFIER | silent_mutation | Average:78.322; most accessible tissue: Minghui63 panicle, score: 94.794 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0514453167 | NA | 1.38E-06 | mr1678 | 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 |
| vg0514453167 | 2.97E-06 | NA | mr1637_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 |
| vg0514453167 | 1.44E-06 | NA | mr1828_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 |