| Variant ID: vg0920188922 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 20188922 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 218. )
GAGAAGATATGTAAAACAAGATGAGCCATTAGCGCTTGATGATTTGAGTATTAATTATTTTAAACTTAACAAATGAATTAATATGATTTTCTAAAAGCAA[T/C]
TTTTCCATAAAAAAAAGTTTTAGAAATCACATCGTTTAGCAATTGGGAAGCATGTGCGTGAAAAAGAGATATTTTTCTTCCCTTCATGGAAAGCCATAGT
ACTATGGCTTTCCATGAAGGGAAGAAAAATATCTCTTTTTCACGCACATGCTTCCCAATTGCTAAACGATGTGATTTCTAAAACTTTTTTTTATGGAAAA[A/G]
TTGCTTTTAGAAAATCATATTAATTCATTTGTTAAGTTTAAAATAATTAATACTCAAATCATCAAGCGCTAATGGCTCATCTTGTTTTACATATCTTCTC
| 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 | 86.80% | 3.60% | 6.37% | 3.24% | NA |
| All Indica | 2759 | 82.20% | 1.40% | 10.80% | 5.55% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 56.50% | 43.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 70.60% | 0.00% | 25.38% | 4.03% | NA |
| Indica II | 465 | 87.10% | 0.60% | 7.31% | 4.95% | NA |
| Indica III | 913 | 87.60% | 2.00% | 3.18% | 7.23% | NA |
| Indica Intermediate | 786 | 81.80% | 2.40% | 10.69% | 5.09% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0920188922 | T -> DEL | N | N | silent_mutation | Average:38.771; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0920188922 | T -> C | LOC_Os09g34190.1 | upstream_gene_variant ; 2615.0bp to feature; MODIFIER | silent_mutation | Average:38.771; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg0920188922 | T -> C | LOC_Os09g34200.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.771; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0920188922 | NA | 6.81E-06 | mr1654 | 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 |
| vg0920188922 | 3.27E-06 | NA | mr1406_2 | 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 |
| vg0920188922 | NA | 1.29E-06 | mr1603_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 |
| vg0920188922 | NA | 1.15E-09 | mr1818_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 |