Variant ID: vg0702869915 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 2869915 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 73. )
TCTCTACTATTATATATAAAAATTAAAGATGTTTTTGCCGGTATTTTGGTACGTTATCCGTGTATGAGTATGTTTTTAAGTTCATTTGGTTTTGGAAATA[C/T]
ATATCCATATTTGAATCGGTTCTTAAGTTCGTTTGCTTTTGGTAATACAGAAGGAATTGTATAAAAAATCTGTCTAAAAAAACTCGCATATTAACTTGAG
CTCAAGTTAATATGCGAGTTTTTTTAGACAGATTTTTTATACAATTCCTTCTGTATTACCAAAAGCAAACGAACTTAAGAACCGATTCAAATATGGATAT[G/A]
TATTTCCAAAACCAAATGAACTTAAAAACATACTCATACACGGATAACGTACCAAAATACCGGCAAAAACATCTTTAATTTTTATATATAATAGTAGAGA
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 | 90.50% | 9.00% | 0.51% | 0.00% | NA |
All Indica | 2759 | 84.40% | 14.80% | 0.87% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.00% | 1.20% | 0.84% | 0.00% | NA |
Indica II | 465 | 54.20% | 43.70% | 2.15% | 0.00% | NA |
Indica III | 913 | 93.80% | 5.80% | 0.44% | 0.00% | NA |
Indica Intermediate | 786 | 81.00% | 18.30% | 0.64% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | 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 | 86.70% | 13.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0702869915 | C -> T | LOC_Os07g05940.1 | upstream_gene_variant ; 771.0bp to feature; MODIFIER | silent_mutation | Average:40.756; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
vg0702869915 | C -> T | LOC_Os07g05930-LOC_Os07g05940 | intergenic_region ; MODIFIER | silent_mutation | Average:40.756; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0702869915 | NA | 9.38E-06 | mr1158_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 |
vg0702869915 | NA | 1.06E-06 | mr1158_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 |
vg0702869915 | NA | 4.54E-06 | mr1296_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 |
vg0702869915 | NA | 7.90E-12 | mr1383_2 | 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 |