| Variant ID: vg1220567760 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20567760 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTAGTACTAGTTGAAAATCCGAAGAAGGAAGAACGGAGTAAACCTTTTGCAAATAGCATTAGGGGAAGGAGAAAAAGGAACTTTCGCAAATAGTTTTATT[C/T]
ATAAAATATGTCCTTAGGTTTTATCCACTTGGCTTATCCTACAGTCAACCTGGCTCTGATACCAGCTTGTCGCGACCGGGAAAATTGCCTTTTCCCGAAC
GTTCGGGAAAAGGCAATTTTCCCGGTCGCGACAAGCTGGTATCAGAGCCAGGTTGACTGTAGGATAAGCCAAGTGGATAAAACCTAAGGACATATTTTAT[G/A]
AATAAAACTATTTGCGAAAGTTCCTTTTTCTCCTTCCCCTAATGCTATTTGCAAAAGGTTTACTCCGTTCTTCCTTCTTCGGATTTTCAACTAGTACTAG
| 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 | 26.30% | 5.00% | 34.83% | 33.81% | NA |
| All Indica | 2759 | 2.80% | 4.30% | 44.94% | 47.95% | NA |
| All Japonica | 1512 | 73.10% | 0.30% | 15.08% | 11.51% | NA |
| Aus | 269 | 2.20% | 37.90% | 38.29% | 21.56% | NA |
| Indica I | 595 | 3.20% | 2.70% | 35.29% | 58.82% | NA |
| Indica II | 465 | 4.50% | 1.90% | 35.70% | 57.85% | NA |
| Indica III | 913 | 1.40% | 8.30% | 56.41% | 33.84% | NA |
| Indica Intermediate | 786 | 2.90% | 2.40% | 44.40% | 50.25% | NA |
| Temperate Japonica | 767 | 88.40% | 0.10% | 3.00% | 8.47% | NA |
| Tropical Japonica | 504 | 55.80% | 0.40% | 30.75% | 13.10% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.40% | 20.75% | 17.84% | NA |
| VI/Aromatic | 96 | 22.90% | 10.40% | 53.12% | 13.54% | NA |
| Intermediate | 90 | 38.90% | 1.10% | 26.67% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220567760 | C -> DEL | N | N | silent_mutation | Average:5.669; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg1220567760 | C -> T | LOC_Os12g34050.1 | upstream_gene_variant ; 483.0bp to feature; MODIFIER | silent_mutation | Average:5.669; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| vg1220567760 | C -> T | LOC_Os12g34050-LOC_Os12g34052 | intergenic_region ; MODIFIER | silent_mutation | Average:5.669; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1220567760 | 1.54E-15 | 7.04E-98 | mr1334 | 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 |
| vg1220567760 | 1.32E-08 | 4.96E-13 | mr1334 | 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 |
| vg1220567760 | 1.03E-17 | 1.58E-106 | mr1334_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 |
| vg1220567760 | 2.96E-09 | 3.48E-12 | mr1334_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 |
| vg1220567760 | 5.25E-08 | 3.89E-55 | mr1991_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 |