| Variant ID: vg1128946610 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28946610 |
| 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: 232. )
CAGTATCTTTCAACATGTCGCCACCCCACATGTCACAATCATCGCCAAAATAAAAGAGTGGCAGCTGCATAGGCAAAAGTGGGGGTTGTCTACCTTAGGG[G/A]
GTTCGCTGTTTCGGGAAAAATTACCTAAGACTCTCTTTTTGTGGGTTCCTACCTATTTAGAAGCCATGTACCTATCTTTTGCCCCTGCTCTATCAGTATA
TATACTGATAGAGCAGGGGCAAAAGATAGGTACATGGCTTCTAAATAGGTAGGAACCCACAAAAAGAGAGTCTTAGGTAATTTTTCCCGAAACAGCGAAC[C/T]
CCCTAAGGTAGACAACCCCCACTTTTGCCTATGCAGCTGCCACTCTTTTATTTTGGCGATGATTGTGACATGTGGGGTGGCGACATGTTGAAAGATACTG
| 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 | 96.90% | 3.00% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 4.00% | 0.26% | 0.00% | NA |
| Aus | 269 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 94.30% | 5.30% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 96.00% | 3.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1128946610 | G -> A | LOC_Os11g48000.1 | downstream_gene_variant ; 689.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1128946610 | G -> A | LOC_Os11g47990-LOC_Os11g48000 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128946610 | 3.22E-06 | 3.22E-06 | mr1721 | Jap_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 |
| vg1128946610 | 6.40E-06 | 6.40E-06 | mr1861 | Jap_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 |
| vg1128946610 | 4.81E-06 | 4.80E-06 | mr1952 | Jap_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 |