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Detailed information for vg0720057946:

Variant ID: vg0720057946 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20057946
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: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTGGCGAGAAGAGCATTGTACTCCTCTTCCATAGCAGTGCACCAATGGGGGTCCGCCAAGGCCGCACGATAGGTGCGAGGCACCGGCGACAAGGGTGC[G/A]
GCGTGGAGGTTGAGGCGATCGATCGGTCGTCGTATGCCAGATTTGCCACGCGTGACCATGGCATGTTCATTGTCGGCCGGAGAAGCATCGAGGATCGGTG

Reverse complement sequence

CACCGATCCTCGATGCTTCTCCGGCCGACAATGAACATGCCATGGTCACGCGTGGCAAATCTGGCATACGACGACCGATCGATCGCCTCAACCTCCACGC[C/T]
GCACCCTTGTCGCCGGTGCCTCGCACCTATCGTGCGGCCTTGGCGGACCCCCATTGGTGCACTGCTATGGAAGAGGAGTACAATGCTCTTCTCGCCAACC

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 53.70% 15.20% 1.12% 29.98% NA
All Indica  2759 22.50% 25.40% 1.92% 50.13% NA
All Japonica  1512 99.30% 0.20% 0.00% 0.46% NA
Aus  269 96.30% 0.40% 0.00% 3.35% NA
Indica I  595 11.90% 39.50% 1.01% 47.56% NA
Indica II  465 23.20% 22.80% 3.01% 50.97% NA
Indica III  913 23.10% 20.60% 1.86% 54.44% NA
Indica Intermediate  786 29.50% 21.90% 2.04% 46.56% NA
Temperate Japonica  767 99.00% 0.30% 0.00% 0.78% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 68.90% 11.10% 0.00% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0720057946 G -> DEL LOC_Os07g33570.1 N frameshift_variant Average:34.545; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 N N N N
vg0720057946 G -> A LOC_Os07g33570.1 synonymous_variant ; p.Ala412Ala; LOW synonymous_codon Average:34.545; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720057946 NA 2.39E-09 mr1486 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
vg0720057946 NA 9.92E-07 mr1548 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
vg0720057946 NA 4.47E-08 mr1721 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
vg0720057946 NA 2.58E-08 mr1486_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
vg0720057946 2.21E-06 NA mr1721_2 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
vg0720057946 5.02E-06 7.69E-09 mr1721_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