| Variant ID: vg0907518119 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 7518119 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 107. )
TTACAAGCAAGCTACGCAGTGTGGGGCACCTCCATCGCGCCTCTACCATGGACCTCCCGCAGGCTCTGATACCACTTGTTATAAAACCAGCCCCGAAATC[G/A]
ACATCGGTAGCTAAACGCGGAAGAAAACACCATAGGAGATCCAAAACGATGACTACACCGAGACACGATATTTGGTAATGGAGTTCAGCCGTAGCCTACA
TGTAGGCTACGGCTGAACTCCATTACCAAATATCGTGTCTCGGTGTAGTCATCGTTTTGGATCTCCTATGGTGTTTTCTTCCGCGTTTAGCTACCGATGT[C/T]
GATTTCGGGGCTGGTTTTATAACAAGTGGTATCAGAGCCTGCGGGAGGTCCATGGTAGAGGCGCGATGGAGGTGCCCCACACTGCGTAGCTTGCTTGTAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.60% | 0.80% | 17.96% | 12.61% | NA |
| All Indica | 2759 | 60.90% | 1.00% | 24.03% | 14.03% | NA |
| All Japonica | 1512 | 79.70% | 0.40% | 7.74% | 12.17% | NA |
| Aus | 269 | 69.50% | 0.70% | 23.05% | 6.69% | NA |
| Indica I | 595 | 42.00% | 1.70% | 33.11% | 23.19% | NA |
| Indica II | 465 | 83.90% | 1.10% | 9.68% | 5.38% | NA |
| Indica III | 913 | 63.30% | 0.20% | 25.85% | 10.62% | NA |
| Indica Intermediate | 786 | 58.90% | 1.40% | 23.54% | 16.16% | NA |
| Temperate Japonica | 767 | 91.10% | 0.50% | 3.13% | 5.22% | NA |
| Tropical Japonica | 504 | 77.40% | 0.20% | 9.72% | 12.70% | NA |
| Japonica Intermediate | 241 | 48.10% | 0.40% | 18.26% | 33.20% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 1.10% | 5.56% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0907518119 | G -> DEL | N | N | silent_mutation | Average:55.273; most accessible tissue: Minghui63 young leaf, score: 80.883 | N | N | N | N |
| vg0907518119 | G -> A | LOC_Os09g13030.1 | upstream_gene_variant ; 2365.0bp to feature; MODIFIER | silent_mutation | Average:55.273; most accessible tissue: Minghui63 young leaf, score: 80.883 | N | N | N | N |
| vg0907518119 | G -> A | LOC_Os09g13040.1 | upstream_gene_variant ; 921.0bp to feature; MODIFIER | silent_mutation | Average:55.273; most accessible tissue: Minghui63 young leaf, score: 80.883 | N | N | N | N |
| vg0907518119 | G -> A | LOC_Os09g13030-LOC_Os09g13040 | intergenic_region ; MODIFIER | silent_mutation | Average:55.273; most accessible tissue: Minghui63 young leaf, score: 80.883 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0907518119 | NA | 6.88E-06 | mr1360_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 |
| vg0907518119 | NA | 9.50E-08 | mr1895_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 |
| vg0907518119 | NA | 3.51E-09 | mr1895_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 |
| vg0907518119 | NA | 9.29E-07 | mr1931_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 |