| Variant ID: vg1105512758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5512758 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGGTTGAGAGTGATATTTTATTGTTCTTTTTAAGTAGTGGCATTTGGCCACGAAGCCACTTTTGATGATGGTGTAATCCTAAATTTCTCCTTTAGTTAT[G/A]
GGTATATAATTCAAGAAATTTTCCACTAATGTTGTATCGGGCATATGAGGTAATGTACTAAGGGCCCCTTTGAATCGCGGGATTGAGAAAACGTAGGAAT
ATTCCTACGTTTTCTCAATCCCGCGATTCAAAGGGGCCCTTAGTACATTACCTCATATGCCCGATACAACATTAGTGGAAAATTTCTTGAATTATATACC[C/T]
ATAACTAAAGGAGAAATTTAGGATTACACCATCATCAAAAGTGGCTTCGTGGCCAAATGCCACTACTTAAAAAGAACAATAAAATATCACTCTCAACCAG
| 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 | 92.30% | 4.80% | 0.06% | 2.84% | NA |
| All Indica | 2759 | 88.70% | 6.80% | 0.11% | 4.42% | NA |
| All Japonica | 1512 | 98.40% | 0.90% | 0.00% | 0.73% | NA |
| Aus | 269 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 84.40% | 4.40% | 0.17% | 11.09% | NA |
| Indica II | 465 | 96.30% | 3.00% | 0.00% | 0.65% | NA |
| Indica III | 913 | 91.90% | 3.80% | 0.22% | 4.05% | NA |
| Indica Intermediate | 786 | 83.70% | 14.20% | 0.00% | 2.04% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 2.40% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105512758 | G -> A | LOC_Os11g10160.1 | upstream_gene_variant ; 691.0bp to feature; MODIFIER | silent_mutation | Average:56.042; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
| vg1105512758 | G -> A | LOC_Os11g10170.1 | upstream_gene_variant ; 1826.0bp to feature; MODIFIER | silent_mutation | Average:56.042; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
| vg1105512758 | G -> A | LOC_Os11g10160-LOC_Os11g10170 | intergenic_region ; MODIFIER | silent_mutation | Average:56.042; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
| vg1105512758 | G -> DEL | N | N | silent_mutation | Average:56.042; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105512758 | NA | 8.34E-06 | mr1229 | 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 |
| vg1105512758 | 3.51E-06 | 3.51E-06 | mr1468 | 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 |
| vg1105512758 | NA | 6.15E-09 | mr1723_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 |