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Detailed information for vg1016071802:

Variant ID: vg1016071802 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16071802
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TATTAGCGCATGATTAATTAACTATTAGCTAATTTTTTTCAAAAATATATTAATTTGATTTTTAAGCAACTTTCGTATATAAACTTTTTGTAAAAAAAAC[G/A]
CACCGTTTAGCAGTTTGAAAAGCGTGTGCGTGGAAAACAAGGGAGAGGGGTTGGGAAGAGGGTGAAACGAACGCAGCCTGAAAGAGGGTGGGAGCGGGGT

Reverse complement sequence

ACCCCGCTCCCACCCTCTTTCAGGCTGCGTTCGTTTCACCCTCTTCCCAACCCCTCTCCCTTGTTTTCCACGCACACGCTTTTCAAACTGCTAAACGGTG[C/T]
GTTTTTTTTACAAAAAGTTTATATACGAAAGTTGCTTAAAAATCAAATTAATATATTTTTGAAAAAAATTAGCTAATAGTTAATTAATCATGCGCTAATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 2.40% 0.72% 0.00% NA
All Indica  2759 95.00% 3.90% 1.16% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 86.60% 10.40% 3.03% 0.00% NA
Indica II  465 95.30% 3.70% 1.08% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 3.40% 1.15% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1016071802 G -> A LOC_Os10g30840-LOC_Os10g30850 intergenic_region ; MODIFIER silent_mutation Average:70.638; most accessible tissue: Minghui63 panicle, score: 87.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016071802 NA 6.26E-07 mr1038 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
vg1016071802 6.10E-06 2.93E-06 mr1281 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
vg1016071802 7.33E-07 1.33E-07 mr1344 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
vg1016071802 NA 4.15E-08 mr1389 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
vg1016071802 9.91E-08 7.21E-09 mr1538 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
vg1016071802 NA 9.80E-06 mr1547 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
vg1016071802 NA 1.75E-06 mr1982 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