| Variant ID: vg0220187125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20187125 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCAGACCAGCCACGCAATGCCGGTCAGACCGCCCTGTCTGCACGGTCAGACCGGCCATGCAAAGCCGGTCAGACCGCCGGTACCACCGGTCAGACCAGCC[A/G]
TGCAATGCCAGTCAGACCGCCCCTGGTCTATGGTTTTACCAATTTCGTCCAAAGTTTTGAAATCAAGCATCGGCCTTCAGTATATAATTTTTCTTCACAT
ATGTGAAGAAAAATTATATACTGAAGGCCGATGCTTGATTTCAAAACTTTGGACGAAATTGGTAAAACCATAGACCAGGGGCGGTCTGACTGGCATTGCA[T/C]
GGCTGGTCTGACCGGTGGTACCGGCGGTCTGACCGGCTTTGCATGGCCGGTCTGACCGTGCAGACAGGGCGGTCTGACCGGCATTGCGTGGCTGGTCTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.40% | 5.50% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 95.80% | 4.10% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.40% | 7.40% | 1.12% | 0.00% | NA |
| Indica I | 595 | 94.80% | 5.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.80% | 6.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0220187125 | A -> G | LOC_Os02g33860.1 | downstream_gene_variant ; 989.0bp to feature; MODIFIER | silent_mutation | Average:52.517; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |
| vg0220187125 | A -> G | LOC_Os02g33860-LOC_Os02g33890 | intergenic_region ; MODIFIER | silent_mutation | Average:52.517; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220187125 | 2.08E-06 | NA | mr1202 | 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 |
| vg0220187125 | 1.13E-06 | NA | mr1768 | 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 |