| Variant ID: vg0913499937 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 13499937 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.03, others allele: 0.00, population size: 36. )
AGATAGACCATCAATAATGCAAAAACAATTATTTTGTATACAATTTTAAACATCCACGCAATTTATTATTGTGTTGTCTTAATGAGATGTCTTGATAATG[A/G]
GATGATGAACAATTATGACAAAAAAATGGTACTGCAAGATTAACATATTCCATACGTGAGGGCAGAATTAAGGGTAGTTTTTTGTTTTCTATCGTACTAA
TTAGTACGATAGAAAACAAAAAACTACCCTTAATTCTGCCCTCACGTATGGAATATGTTAATCTTGCAGTACCATTTTTTTGTCATAATTGTTCATCATC[T/C]
CATTATCAAGACATCTCATTAAGACAACACAATAATAAATTGCGTGGATGTTTAAAATTGTATACAAAATAATTGTTTTTGCATTATTGATGGTCTATCT
| 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 | 36.30% | 23.60% | 7.15% | 32.97% | NA |
| All Indica | 2759 | 9.20% | 37.40% | 3.33% | 50.05% | NA |
| All Japonica | 1512 | 90.80% | 2.80% | 1.12% | 5.22% | NA |
| Aus | 269 | 14.50% | 4.10% | 62.08% | 19.33% | NA |
| Indica I | 595 | 17.30% | 16.60% | 2.35% | 63.70% | NA |
| Indica II | 465 | 15.10% | 50.30% | 5.59% | 29.03% | NA |
| Indica III | 913 | 0.80% | 43.30% | 1.53% | 54.44% | NA |
| Indica Intermediate | 786 | 9.50% | 38.50% | 4.83% | 47.07% | NA |
| Temperate Japonica | 767 | 95.40% | 1.80% | 0.65% | 2.09% | NA |
| Tropical Japonica | 504 | 82.70% | 5.60% | 0.79% | 10.91% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.40% | 3.32% | 3.32% | NA |
| VI/Aromatic | 96 | 4.20% | 12.50% | 54.17% | 29.17% | NA |
| Intermediate | 90 | 51.10% | 17.80% | 11.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0913499937 | A -> G | LOC_Os09g22340.1 | upstream_gene_variant ; 2733.0bp to feature; MODIFIER | silent_mutation | Average:16.72; most accessible tissue: Callus, score: 60.925 | N | N | N | N |
| vg0913499937 | A -> G | LOC_Os09g22340-LOC_Os09g22350 | intergenic_region ; MODIFIER | silent_mutation | Average:16.72; most accessible tissue: Callus, score: 60.925 | N | N | N | N |
| vg0913499937 | A -> DEL | N | N | silent_mutation | Average:16.72; most accessible tissue: Callus, score: 60.925 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0913499937 | 1.20E-06 | NA | mr1343 | 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 |
| vg0913499937 | NA | 3.45E-10 | mr1827 | 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 |
| vg0913499937 | NA | 6.47E-10 | mr1927 | 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 |
| vg0913499937 | NA | 1.26E-06 | mr1559_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 |