| Variant ID: vg1119711986 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19711986 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 222. )
CTGTAAAGAAAAACTCGACCAGCCACCTTTGGCATAATATTCAACAACGGAATTTGCAGTTCCACTAAGTAGGGACAAATGAGGAAACCAATAGCATTTC[A/G,C]
AAGTGTCAGGAAACAAACTTTCAATATGTTGCATGTCAGTCACTAAGTTTTTCAATTCATGATAAATAATACTACGATTAAATATAGATGAGTTGACAGT
ACTGTCAACTCATCTATATTTAATCGTAGTATTATTTATCATGAATTGAAAAACTTAGTGACTGACATGCAACATATTGAAAGTTTGTTTCCTGACACTT[T/C,G]
GAAATGCTATTGGTTTCCTCATTTGTCCCTACTTAGTGGAACTGCAAATTCCGTTGTTGAATATTATGCCAAAGGTGGCTGGTCGAGTTTTTCTTTACAG
| 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 | 58.80% | 40.80% | 0.42% | 0.00% | C: 0.04% |
| All Indica | 2759 | 85.30% | 14.30% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 6.30% | 93.30% | 0.33% | 0.00% | C: 0.13% |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.00% | 3.90% | 0.17% | 0.00% | NA |
| Indica II | 465 | 95.50% | 4.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 75.70% | 23.70% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 82.40% | 17.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 9.00% | 90.50% | 0.26% | 0.00% | C: 0.26% |
| Tropical Japonica | 504 | 3.20% | 96.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 20.80% | 78.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 36.70% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119711986 | A -> G | LOC_Os11g33320.1 | downstream_gene_variant ; 2947.0bp to feature; MODIFIER | silent_mutation | Average:47.957; most accessible tissue: Callus, score: 71.812 | N | N | N | N |
| vg1119711986 | A -> G | LOC_Os11g33330.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.957; most accessible tissue: Callus, score: 71.812 | N | N | N | N |
| vg1119711986 | A -> C | LOC_Os11g33320.1 | downstream_gene_variant ; 2947.0bp to feature; MODIFIER | silent_mutation | Average:47.957; most accessible tissue: Callus, score: 71.812 | N | N | N | N |
| vg1119711986 | A -> C | LOC_Os11g33330.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.957; most accessible tissue: Callus, score: 71.812 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119711986 | NA | 4.04E-18 | mr1242 | 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 |
| vg1119711986 | NA | 5.62E-06 | mr1704 | 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 |
| vg1119711986 | NA | 1.03E-18 | mr1239_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 |
| vg1119711986 | NA | 1.12E-06 | mr1717_2 | 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 |