| Variant ID: vg0712894798 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12894798 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCGTCTGCGCCGTTTATCTTTTTTTTCCGCTGCTTAGATCTTTATTGATTGAGAGGAACTGTCTACCTCTGTAATGACATTTTATTCGCTTATTAATTA[T/G]
AGTAATAATTGTACTCTATTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGACGAGGGTTCACACACATGTAAGCGTTTGGAATTTTGGATAGAA
TTCTATCCAAAATTCCAAACGCTTACATGTGTGTGAACCCTCGTCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAATAGAGTACAATTATTACT[A/C]
TAATTAATAAGCGAATAAAATGTCATTACAGAGGTAGACAGTTCCTCTCAATCAATAAAGATCTAAGCAGCGGAAAAAAAAGATAAACGGCGCAGACGGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.70% | 25.20% | 0.85% | 9.29% | NA |
| All Indica | 2759 | 96.90% | 1.10% | 0.14% | 1.88% | NA |
| All Japonica | 1512 | 6.30% | 74.70% | 0.33% | 18.72% | NA |
| Aus | 269 | 79.60% | 0.00% | 9.67% | 10.78% | NA |
| Indica I | 595 | 99.30% | 0.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 91.70% | 1.50% | 0.25% | 6.49% | NA |
| Temperate Japonica | 767 | 2.00% | 65.80% | 0.52% | 31.68% | NA |
| Tropical Japonica | 504 | 13.50% | 85.90% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 5.00% | 79.30% | 0.41% | 15.35% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 3.12% | 72.92% | NA |
| Intermediate | 90 | 55.60% | 36.70% | 2.22% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712894798 | T -> DEL | N | N | silent_mutation | Average:26.883; most accessible tissue: Minghui63 root, score: 41.911 | N | N | N | N |
| vg0712894798 | T -> G | LOC_Os07g22860.1 | upstream_gene_variant ; 3830.0bp to feature; MODIFIER | silent_mutation | Average:26.883; most accessible tissue: Minghui63 root, score: 41.911 | N | N | N | N |
| vg0712894798 | T -> G | LOC_Os07g22870.1 | upstream_gene_variant ; 877.0bp to feature; MODIFIER | silent_mutation | Average:26.883; most accessible tissue: Minghui63 root, score: 41.911 | N | N | N | N |
| vg0712894798 | T -> G | LOC_Os07g22880.1 | downstream_gene_variant ; 1734.0bp to feature; MODIFIER | silent_mutation | Average:26.883; most accessible tissue: Minghui63 root, score: 41.911 | N | N | N | N |
| vg0712894798 | T -> G | LOC_Os07g22860-LOC_Os07g22870 | intergenic_region ; MODIFIER | silent_mutation | Average:26.883; most accessible tissue: Minghui63 root, score: 41.911 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712894798 | NA | 6.78E-13 | mr1217_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 |
| vg0712894798 | NA | 5.03E-06 | mr1533_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 |
| vg0712894798 | 1.81E-06 | 3.62E-07 | mr1551_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 |