Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1008389212:

Variant ID: vg1008389212 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8389212
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: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTTCATTTCAACCCCTTGCTCATCGTGGGATGTCCAACAATTATAGCTTGGCATGAACCCCGACTCAAACAGGTGGAAATGAATAGTCCTGGATGCAT[A/G]
ATACTCCTTCTGGTTCTTACACTTATTGCATGGACAACAAATAAAACCGTTACGCTTGTTAGCTTCGGCCACTCTCAAAAAATAATGCACGCCCTCGATA

Reverse complement sequence

TATCGAGGGCGTGCATTATTTTTTGAGAGTGGCCGAAGCTAACAAGCGTAACGGTTTTATTTGTTGTCCATGCAATAAGTGTAAGAACCAGAAGGAGTAT[T/C]
ATGCATCCAGGACTATTCATTTCCACCTGTTTGAGTCGGGGTTCATGCCAAGCTATAATTGTTGGACATCCCACGATGAGCAAGGGGTTGAAATGAAAGA

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 93.50% 5.00% 1.54% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 80.20% 15.10% 4.70% 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 99.40% 0.40% 0.22% 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 63.20% 29.20% 7.56% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.50% 2.10% 5.39% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg1008389212 A -> G LOC_Os10g16840.1 missense_variant ; p.Tyr74His; MODERATE nonsynonymous_codon ; Y74H Average:33.115; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 benign 0.819 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008389212 3.20E-15 3.21E-34 mr1768_2 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
vg1008389212 3.86E-07 9.77E-12 mr1768_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