Variant ID: vg1003603685 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 3603685 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 108. )
TCGGGCCACCAACAACCACTTGCACTTCGTGTGGAATATCTTCAACTTGCTTACGCAAGCCCTTCAATATTACCATAGCCCTCTCGTACGCATTATATAT[A/G]
TACTAGCAAAAATGCCCGTGCGTTGCAACGGGTGAAAAAATTCTAATGATAATATACGTTTTTCATGAATAATCATGTCAATGACAATGTTTGTATTTTA
TAAAATACAAACATTGTCATTGACATGATTATTCATGAAAAACGTATATTATCATTAGAATTTTTTCACCCGTTGCAACGCACGGGCATTTTTGCTAGTA[T/C]
ATATATAATGCGTACGAGAGGGCTATGGTAATATTGAAGGGCTTGCGTAAGCAAGTTGAAGATATTCCACACGAAGTGCAAGTGGTTGTTGGTGGCCCGA
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 | 75.40% | 24.50% | 0.08% | 0.00% | NA |
All Indica | 2759 | 66.70% | 33.20% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
Aus | 269 | 91.40% | 8.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 67.40% | 32.40% | 0.17% | 0.00% | NA |
Indica II | 465 | 68.00% | 32.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 72.70% | 27.10% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 58.40% | 41.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 79.20% | 20.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 90.90% | 9.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
Intermediate | 90 | 72.20% | 26.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1003603685 | A -> G | LOC_Os10g06910.1 | downstream_gene_variant ; 3476.0bp to feature; MODIFIER | silent_mutation | Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
vg1003603685 | A -> G | LOC_Os10g06920.1 | downstream_gene_variant ; 1471.0bp to feature; MODIFIER | silent_mutation | Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
vg1003603685 | A -> G | LOC_Os10g06920-LOC_Os10g06930 | intergenic_region ; MODIFIER | silent_mutation | Average:36.657; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1003603685 | 8.26E-09 | 1.03E-16 | mr1709 | 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 |
vg1003603685 | 2.25E-07 | 1.18E-11 | mr1709 | 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 |
vg1003603685 | NA | 1.67E-07 | mr1547_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 |
vg1003603685 | 2.75E-12 | 6.34E-21 | mr1709_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 |
vg1003603685 | 8.17E-11 | 1.63E-18 | mr1709_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 |