Variant ID: vg1013596120 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 13596120 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )
TCATTGTTGCCTGCAGAAGTAACAAAATTGTTTCATATACATACACGAGAATACTATTGATTCCAATGCAAAATAACGGGGTCTAACCTCAGAACACACT[A/G]
ATATGCACAGTACAATCGACCATGCTTGCTGATTTGGCAAGATTCAGGAGAAAAACATGGAGAATTACAGTCATATATGAAGGTAAGTTCAAATAATACC
GGTATTATTTGAACTTACCTTCATATATGACTGTAATTCTCCATGTTTTTCTCCTGAATCTTGCCAAATCAGCAAGCATGGTCGATTGTACTGTGCATAT[T/C]
AGTGTGTTCTGAGGTTAGACCCCGTTATTTTGCATTGGAATCAATAGTATTCTCGTGTATGTATATGAAACAATTTTGTTACTTCTGCAGGCAACAATGA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.60% | 1.90% | 0.47% | 0.00% | NA |
All Indica | 2759 | 95.90% | 3.30% | 0.80% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 89.60% | 7.70% | 2.69% | 0.00% | NA |
Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 94.10% | 5.10% | 0.76% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1013596120 | A -> G | LOC_Os10g26270.1 | upstream_gene_variant ; 1864.0bp to feature; MODIFIER | silent_mutation | Average:42.668; most accessible tissue: Minghui63 root, score: 54.099 | N | N | N | N |
vg1013596120 | A -> G | LOC_Os10g26240.1 | downstream_gene_variant ; 3446.0bp to feature; MODIFIER | silent_mutation | Average:42.668; most accessible tissue: Minghui63 root, score: 54.099 | N | N | N | N |
vg1013596120 | A -> G | LOC_Os10g26250.1 | downstream_gene_variant ; 1839.0bp to feature; MODIFIER | silent_mutation | Average:42.668; most accessible tissue: Minghui63 root, score: 54.099 | N | N | N | N |
vg1013596120 | A -> G | LOC_Os10g26280.1 | downstream_gene_variant ; 4377.0bp to feature; MODIFIER | silent_mutation | Average:42.668; most accessible tissue: Minghui63 root, score: 54.099 | N | N | N | N |
vg1013596120 | A -> G | LOC_Os10g26260.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.668; most accessible tissue: Minghui63 root, score: 54.099 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1013596120 | 3.73E-08 | 2.38E-08 | mr1533 | 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 |
vg1013596120 | 1.19E-09 | 1.12E-09 | mr1980 | 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 |
vg1013596120 | 8.32E-07 | 1.78E-08 | mr1533_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 |