| Variant ID: vg0910979875 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10979875 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 313. )
AGCTATGAAAAGTTAAAGGCCTGCTTGACACTAAAAACTATGGTATTCAAATATTGTGGCATATCGATATTTTACTATCCAAACAGGCCCTAAACTAGGA[A/T]
AAATACAGATATAATAAAATGTGCGATGTACTCCAAATTAGAGAAGGAAATGTTCACAAACAAACCCAGAAGTCTTCCTCAACACGATGGAGACAGCTTG
CAAGCTGTCTCCATCGTGTTGAGGAAGACTTCTGGGTTTGTTTGTGAACATTTCCTTCTCTAATTTGGAGTACATCGCACATTTTATTATATCTGTATTT[T/A]
TCCTAGTTTAGGGCCTGTTTGGATAGTAAAATATCGATATGCCACAATATTTGAATACCATAGTTTTTAGTGTCAAGCAGGCCTTTAACTTTTCATAGCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.20% | 3.60% | 4.30% | 11.85% | NA |
| All Indica | 2759 | 70.30% | 6.00% | 6.49% | 17.22% | NA |
| All Japonica | 1512 | 94.00% | 0.20% | 1.46% | 4.37% | NA |
| Aus | 269 | 94.10% | 0.70% | 0.37% | 4.83% | NA |
| Indica I | 595 | 76.00% | 2.40% | 6.22% | 15.46% | NA |
| Indica II | 465 | 61.50% | 11.40% | 5.81% | 21.29% | NA |
| Indica III | 913 | 71.50% | 3.70% | 6.35% | 18.40% | NA |
| Indica Intermediate | 786 | 69.70% | 8.30% | 7.25% | 14.76% | NA |
| Temperate Japonica | 767 | 95.30% | 0.30% | 1.69% | 2.74% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.79% | 3.77% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.40% | 2.07% | 10.79% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 1.11% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910979875 | A -> DEL | N | N | silent_mutation | Average:49.092; most accessible tissue: Zhenshan97 young leaf, score: 89.559 | N | N | N | N |
| vg0910979875 | A -> T | LOC_Os09g17920.1 | upstream_gene_variant ; 4962.0bp to feature; MODIFIER | silent_mutation | Average:49.092; most accessible tissue: Zhenshan97 young leaf, score: 89.559 | N | N | N | N |
| vg0910979875 | A -> T | LOC_Os09g17940.1 | downstream_gene_variant ; 3491.0bp to feature; MODIFIER | silent_mutation | Average:49.092; most accessible tissue: Zhenshan97 young leaf, score: 89.559 | N | N | N | N |
| vg0910979875 | A -> T | LOC_Os09g17930.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.092; most accessible tissue: Zhenshan97 young leaf, score: 89.559 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910979875 | NA | 1.61E-06 | mr1815_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 |
| vg0910979875 | 6.81E-06 | 6.81E-06 | mr1966_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 |
| vg0910979875 | 3.73E-06 | 3.73E-06 | mr1991_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 |