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Detailed information for vg0139966622:

Variant ID: vg0139966622 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39966622
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGTTCATAAAATACTTACATGATTGACTTATGAGATGTGTCAGGATGCAATATCAGATCATCACATGATACAGACTCCCCTTCTTCATTGTCATCCA[A/G]
AGGCCAATAGGTGTCACCTCCATTAGTGCTTTTGAAAAGTCTCATCACAGGTCGGTATATAAGAAAAGCAACCTAGATTGAAGTGAAAGTATTAGTACGC

Reverse complement sequence

GCGTACTAATACTTTCACTTCAATCTAGGTTGCTTTTCTTATATACCGACCTGTGATGAGACTTTTCAAAAGCACTAATGGAGGTGACACCTATTGGCCT[T/C]
TGGATGACAATGAAGAAGGGGAGTCTGTATCATGTGATGATCTGATATTGCATCCTGACACATCTCATAAGTCAATCATGTAAGTATTTTATGAACATCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.60% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.20% 4.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 86.90% 12.90% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg0139966622 A -> G LOC_Os01g68810.1 synonymous_variant ; p.Leu880Leu; LOW synonymous_codon Average:55.104; most accessible tissue: Minghui63 flower, score: 68.171 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139966622 NA 3.29E-07 mr1471 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
vg0139966622 NA 3.71E-06 mr1642 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
vg0139966622 NA 9.74E-06 mr1819_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
vg0139966622 NA 3.68E-06 mr1850_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
vg0139966622 4.21E-06 4.21E-06 mr1885_2 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