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Detailed information for vg0416659011:

Variant ID: vg0416659011 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16659011
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


AACAACATAAGTCTAGACATACCCAATCTGGCACCATAAGGGCCGACATGAGGGATGAAGACTATACTAGCCGTTGACTATGTGTTGGAGATCCATGCCG[G/A]
CAAGTCGACGCCGACTAGATTAGGTCATCCCAGCTATTGTGCTCGTGTGATACTGATATATAAAGGCAACACCGACTGTGGAGATTATGGGTACCACATA

Reverse complement sequence

TATGTGGTACCCATAATCTCCACAGTCGGTGTTGCCTTTATATATCAGTATCACACGAGCACAATAGCTGGGATGACCTAATCTAGTCGGCGTCGACTTG[C/T]
CGGCATGGATCTCCAACACATAGTCAACGGCTAGTATAGTCTTCATCCCTCATGTCGGCCCTTATGGTGCCAGATTGGGTATGTCTAGACTTATGTTGTT

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 97.70% 1.60% 0.63% 0.00% NA
All Indica  2759 99.30% 0.40% 0.29% 0.00% NA
All Japonica  1512 94.20% 4.40% 1.39% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 0.80% 0.67% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.60% 0.25% 0.00% NA
Temperate Japonica  767 91.00% 6.90% 2.09% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 4.10% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0416659011 G -> A LOC_Os04g28190-LOC_Os04g28210 intergenic_region ; MODIFIER silent_mutation Average:64.771; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416659011 2.73E-06 NA mr1549 Jap_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
vg0416659011 NA 4.21E-06 mr1550 Jap_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
vg0416659011 7.95E-07 1.36E-10 mr1757 Jap_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
vg0416659011 NA 1.09E-06 mr1549_2 Jap_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