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Detailed information for vg0334841623:

Variant ID: vg0334841623 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34841623
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.71, A: 0.29, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGGTCTCGCAGAAGGGGGGCCGAGAGCAGCCCCCAGTCTCGCGGGGGATCCAGCAGTACCCCGTCGTCCCGGGGGCGGACCGCGGCCTTTTCCTCCCC[A/G]
ACTCCGGCGAGTATGGAGCCACTTCTGCAGGTGCTCGCCGCCGCCGACTACACTGTACGAGAGGGGTTGAACACCCAAGTTCAAGCCCTAGCGGAAGAGC

Reverse complement sequence

GCTCTTCCGCTAGGGCTTGAACTTGGGTGTTCAACCCCTCTCGTACAGTGTAGTCGGCGGCGGCGAGCACCTGCAGAAGTGGCTCCATACTCGCCGGAGT[T/C]
GGGGAGGAAAAGGCCGCGGTCCGCCCCCGGGACGACGGGGTACTGCTGGATCCCCCGCGAGACTGGGGGCTGCTCTCGGCCCCCCTTCTGCGAGACCAGC

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 53.00% 25.70% 21.18% 0.06% NA
All Indica  2759 23.50% 41.60% 34.83% 0.11% NA
All Japonica  1512 99.30% 0.30% 0.40% 0.00% NA
Aus  269 77.70% 18.20% 4.09% 0.00% NA
Indica I  595 12.40% 36.10% 51.09% 0.34% NA
Indica II  465 22.80% 40.40% 36.77% 0.00% NA
Indica III  913 24.80% 49.20% 25.96% 0.11% NA
Indica Intermediate  786 30.80% 37.50% 31.68% 0.00% NA
Temperate Japonica  767 99.50% 0.30% 0.26% 0.00% NA
Tropical Japonica  504 99.00% 0.20% 0.79% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 2.10% 3.12% 0.00% NA
Intermediate  90 64.40% 13.30% 22.22% 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
vg0334841623 A -> DEL LOC_Os03g61390.1 N frameshift_variant Average:68.665; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N
vg0334841623 A -> G LOC_Os03g61390.1 synonymous_variant ; p.Pro215Pro; LOW synonymous_codon Average:68.665; most accessible tissue: Minghui63 young leaf, score: 86.015 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334841623 6.90E-07 6.89E-07 mr1313 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
vg0334841623 7.79E-06 7.79E-06 mr1313 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
vg0334841623 1.98E-06 1.98E-06 mr1473 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
vg0334841623 6.28E-06 6.28E-06 mr1473 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
vg0334841623 1.41E-06 1.40E-06 mr1664 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
vg0334841623 1.68E-06 1.68E-06 mr1664 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
vg0334841623 8.09E-06 9.02E-06 mr1060_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