| Variant ID: vg0516694037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 16694037 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 100. )
TGATTCCTTCTGTATTACCAAAAGTGAACGATCTTAAAAACCGACTCAAATACGGATATGTATTTCCAAAAGCAAACGAACTTAAAAACTGACTCATACA[C/T]
GGATGACATACCAAAATACCAGCAAAAACATCTTCAATTTTTATAATAGTAGAGATAGAGAAGAGATATAGATTAAAACCAAAACATAAAATTAAAACCG
CGGTTTTAATTTTATGTTTTGGTTTTAATCTATATCTCTTCTCTATCTCTACTATTATAAAAATTGAAGATGTTTTTGCTGGTATTTTGGTATGTCATCC[G/A]
TGTATGAGTCAGTTTTTAAGTTCGTTTGCTTTTGGAAATACATATCCGTATTTGAGTCGGTTTTTAAGATCGTTCACTTTTGGTAATACAGAAGGAATCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.70% | 37.10% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 37.80% | 61.70% | 0.43% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 22.90% | 76.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 60.00% | 40.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 38.60% | 61.20% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 35.20% | 63.70% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 25.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0516694037 | C -> T | LOC_Os05g28510.1 | upstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0516694037 | C -> T | LOC_Os05g28510.2 | upstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0516694037 | C -> T | LOC_Os05g28510.3 | upstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0516694037 | C -> T | LOC_Os05g28510.4 | upstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0516694037 | C -> T | LOC_Os05g28500.1 | downstream_gene_variant ; 2955.0bp to feature; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| vg0516694037 | C -> T | LOC_Os05g28500-LOC_Os05g28510 | intergenic_region ; MODIFIER | silent_mutation | Average:36.78; most accessible tissue: Zhenshan97 root, score: 50.453 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0516694037 | NA | 1.60E-06 | mr1360_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 |
| vg0516694037 | NA | 7.55E-06 | mr1499_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 |
| vg0516694037 | NA | 2.34E-06 | mr1499_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 |
| vg0516694037 | NA | 8.60E-06 | mr1647_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 |
| vg0516694037 | NA | 7.83E-06 | mr1647_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 |
| vg0516694037 | NA | 5.03E-07 | mr1648_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 |
| vg0516694037 | NA | 5.53E-06 | mr1648_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 |
| vg0516694037 | NA | 5.08E-08 | mr1655_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 |
| vg0516694037 | 9.63E-06 | NA | mr1861_2 | 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 |
| vg0516694037 | NA | 5.50E-08 | mr1861_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 |