| Variant ID: vg1119035040 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19035040 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )
TATGAGGAGTGTTGTTGGTGCACTTTGTAAACACAGAGAGAAGTAATAAAGTTGTCATCTACTTTGAGAGTTCTTCGATTTGTGTTTCACCGGGTTTTCG[G/A]
TGGTCTAACCGGCGACTCATCGGCGGTCAGACCGGCGACGCACCAGCGGTCAGACCGGCTAGAGCGAGGCGGTCAGACCGGCGGCGACTTCACATGCGGC
GCCGCATGTGAAGTCGCCGCCGGTCTGACCGCCTCGCTCTAGCCGGTCTGACCGCTGGTGCGTCGCCGGTCTGACCGCCGATGAGTCGCCGGTTAGACCA[C/T]
CGAAAACCCGGTGAAACACAAATCGAAGAACTCTCAAAGTAGATGACAACTTTATTACTTCTCTCTGTGTTTACAAAGTGCACCAACAACACTCCTCATA
| 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 | 54.10% | 45.40% | 0.49% | 0.04% | NA |
| All Indica | 2759 | 24.70% | 74.60% | 0.69% | 0.07% | NA |
| All Japonica | 1512 | 98.20% | 1.70% | 0.07% | 0.00% | NA |
| Aus | 269 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 10.60% | 87.70% | 1.68% | 0.00% | NA |
| Indica II | 465 | 35.10% | 64.30% | 0.65% | 0.00% | NA |
| Indica III | 913 | 23.80% | 75.70% | 0.33% | 0.22% | NA |
| Indica Intermediate | 786 | 30.30% | 69.30% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 2.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 31.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1119035040 | G -> A | LOC_Os11g32220.1 | downstream_gene_variant ; 1171.0bp to feature; MODIFIER | silent_mutation | Average:63.937; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg1119035040 | G -> A | LOC_Os11g32210-LOC_Os11g32220 | intergenic_region ; MODIFIER | silent_mutation | Average:63.937; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg1119035040 | G -> DEL | N | N | silent_mutation | Average:63.937; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119035040 | NA | 1.08E-06 | mr1044 | 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 |
| vg1119035040 | NA | 1.12E-07 | mr1044 | 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 |
| vg1119035040 | NA | 5.42E-10 | mr1195 | 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 |
| vg1119035040 | NA | 7.42E-11 | mr1281 | 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 |
| vg1119035040 | NA | 1.32E-11 | mr1827 | 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 |