| Variant ID: vg1204022473 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4022473 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTCCAAGTCATCAGATGGTGCTGTCTAACACAGCAGGGATCCGACTATTGGCGACGTGATAATTCTCTTAGGGGCTTACCAAATTTCACTGTTAACAC[C/A]
TGCCCCCAAATTTTGGGCTTATCAAATTTCACTGTTAACACCTGCCCCCAAATTTTGGAGTATGATAACTCATCCTTCAAAATTATATTATTTTTGATCT
AGATCAAAAATAATATAATTTTGAAGGATGAGTTATCATACTCCAAAATTTGGGGGCAGGTGTTAACAGTGAAATTTGATAAGCCCAAAATTTGGGGGCA[G/T]
GTGTTAACAGTGAAATTTGGTAAGCCCCTAAGAGAATTATCACGTCGCCAATAGTCGGATCCCTGCTGTGTTAGACAGCACCATCTGATGACTTGGAGAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 27.50% | 9.30% | 2.92% | 60.28% | NA |
| All Indica | 2759 | 6.80% | 4.50% | 4.02% | 84.70% | NA |
| All Japonica | 1512 | 62.90% | 19.20% | 0.40% | 17.46% | NA |
| Aus | 269 | 10.40% | 7.10% | 6.32% | 76.21% | NA |
| Indica I | 595 | 1.20% | 1.70% | 3.19% | 93.95% | NA |
| Indica II | 465 | 17.20% | 8.20% | 4.52% | 70.11% | NA |
| Indica III | 913 | 4.30% | 3.80% | 4.38% | 87.51% | NA |
| Indica Intermediate | 786 | 7.80% | 5.20% | 3.94% | 83.08% | NA |
| Temperate Japonica | 767 | 83.40% | 11.90% | 0.26% | 4.43% | NA |
| Tropical Japonica | 504 | 42.50% | 27.00% | 0.40% | 30.16% | NA |
| Japonica Intermediate | 241 | 40.20% | 26.60% | 0.83% | 32.37% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 0.00% | 14.58% | NA |
| Intermediate | 90 | 55.60% | 7.80% | 4.44% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204022473 | C -> DEL | N | N | silent_mutation | Average:12.061; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022473 | C -> A | LOC_Os12g07910.1 | downstream_gene_variant ; 3006.0bp to feature; MODIFIER | silent_mutation | Average:12.061; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022473 | C -> A | LOC_Os12g07920.1 | downstream_gene_variant ; 1065.0bp to feature; MODIFIER | silent_mutation | Average:12.061; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022473 | C -> A | LOC_Os12g07930.1 | downstream_gene_variant ; 211.0bp to feature; MODIFIER | silent_mutation | Average:12.061; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| vg1204022473 | C -> A | LOC_Os12g07920-LOC_Os12g07930 | intergenic_region ; MODIFIER | silent_mutation | Average:12.061; most accessible tissue: Callus, score: 54.315 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204022473 | 3.79E-08 | NA | mr1083 | 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 |
| vg1204022473 | 4.07E-06 | NA | mr1264 | 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 |
| vg1204022473 | NA | 2.25E-06 | mr1345 | 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 |
| vg1204022473 | NA | 8.44E-08 | mr1554 | 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 |
| vg1204022473 | 4.41E-06 | NA | mr1831 | 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 |