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Search for Variation information by Variation ID:

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

Detailed information for vg0220941661:

Variant ID: vg0220941661 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20941661
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTTCTCGGTGAGGTCATCCGCGTTTCGACAAGGGTGATAACCAGAGGAGATGTGGTGCTGCGATTGCGGGGCTCAAGAGCGTGCGCGTTCAAGAAGCC[G/A]
GATCGATTTGTGTCGCGACTCCACCCAAATCGTTGTTTATCAGAACCTTTCGGAAGATCAGGAACCCTAGTGCACATCAAATGGATTCACATATGCATGC

Reverse complement sequence

GCATGCATATGTGAATCCATTTGATGTGCACTAGGGTTCCTGATCTTCCGAAAGGTTCTGATAAACAACGATTTGGGTGGAGTCGCGACACAAATCGATC[C/T]
GGCTTCTTGAACGCGCACGCTCTTGAGCCCCGCAATCGCAGCACCACATCTCCTCTGGTTATCACCCTTGTCGAAACGCGGATGACCTCACCGAGAAGGC

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 89.10% 8.80% 1.06% 0.97% NA
All Indica  2759 88.80% 10.10% 0.54% 0.54% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 28.30% 48.00% 12.27% 11.52% NA
Indica I  595 90.10% 9.60% 0.17% 0.17% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 84.40% 14.20% 0.44% 0.88% NA
Indica Intermediate  786 87.00% 10.90% 1.27% 0.76% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 5.20% 1.04% 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
vg0220941661 G -> A LOC_Os02g34900.1 intron_variant ; MODIFIER silent_mutation Average:41.46; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N
vg0220941661 G -> DEL N N silent_mutation Average:41.46; most accessible tissue: Minghui63 young leaf, score: 63.571 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220941661 NA 3.77E-07 mr1004 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
vg0220941661 NA 5.87E-08 mr1006 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
vg0220941661 NA 6.32E-08 mr1052 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
vg0220941661 NA 6.62E-06 mr1073 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
vg0220941661 NA 8.07E-16 mr1496 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
vg0220941661 1.77E-06 1.13E-07 mr1496 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
vg0220941661 NA 6.39E-13 mr1918 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
vg0220941661 NA 3.91E-06 mr1921 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
vg0220941661 NA 1.39E-06 mr1006_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
vg0220941661 2.41E-06 2.06E-07 mr1123_2 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
vg0220941661 1.57E-06 NA mr1242_2 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
vg0220941661 NA 1.71E-09 mr1327_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
vg0220941661 NA 3.91E-14 mr1496_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
vg0220941661 1.16E-07 9.47E-09 mr1496_2 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
vg0220941661 NA 7.85E-09 mr1627_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
vg0220941661 NA 3.78E-06 mr1929_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