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Detailed information for vg0204430393:

Variant ID: vg0204430393 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4430393
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCAGAATCTACTTTTAGTGCTGGGGGAAGAGTTCTAAGTGATTATCGTAGTTCTCTATGCCCAACAATGGTTGAGGCGTTGATATGTGCTTCTAGCT[G/A]
GATTAGAGGCGCTCCAATGATTACGGTACTCACTATTATGCCATGCATATTTAATGCATATTCTCTTCTTAACACATGACATGAGTAGCTGAATTAACTT

Reverse complement sequence

AAGTTAATTCAGCTACTCATGTCATGTGTTAAGAAGAGAATATGCATTAAATATGCATGGCATAATAGTGAGTACCGTAATCATTGGAGCGCCTCTAATC[C/T]
AGCTAGAAGCACATATCAACGCCTCAACCATTGTTGGGCATAGAGAACTACGATAATCACTTAGAACTCTTCCCCCAGCACTAAAAGTAGATTCTGATGA

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 54.90% 8.90% 5.06% 31.15% NA
All Indica  2759 42.70% 14.80% 7.32% 35.23% NA
All Japonica  1512 71.60% 0.40% 1.46% 26.59% NA
Aus  269 78.40% 0.00% 2.60% 18.96% NA
Indica I  595 48.60% 23.50% 15.46% 12.44% NA
Indica II  465 21.70% 15.90% 7.96% 54.41% NA
Indica III  913 43.30% 14.90% 1.86% 39.98% NA
Indica Intermediate  786 50.00% 7.30% 7.12% 35.62% NA
Temperate Japonica  767 98.00% 0.00% 0.00% 1.96% NA
Tropical Japonica  504 35.30% 0.40% 3.37% 60.91% NA
Japonica Intermediate  241 63.10% 1.70% 2.07% 33.20% NA
VI/Aromatic  96 64.60% 0.00% 3.12% 32.29% NA
Intermediate  90 67.80% 8.90% 5.56% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204430393 G -> A LOC_Os02g08340.1 stop_gained ; p.Trp677*; HIGH stop_gained Average:14.184; most accessible tissue: Callus, score: 42.767 N N N N
vg0204430393 G -> DEL LOC_Os02g08340.1 N frameshift_variant Average:14.184; most accessible tissue: Callus, score: 42.767 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204430393 8.43E-09 5.66E-12 mr1191 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
vg0204430393 4.82E-13 3.71E-17 mr1191 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
vg0204430393 1.23E-10 3.34E-14 mr1644 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
vg0204430393 1.31E-14 9.73E-19 mr1644 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
vg0204430393 NA 6.74E-07 mr1662 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
vg0204430393 4.16E-10 2.47E-17 mr1191_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
vg0204430393 7.72E-11 2.64E-22 mr1191_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
vg0204430393 NA 7.97E-06 mr1380_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
vg0204430393 NA 1.40E-06 mr1662_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
vg0204430393 NA 3.11E-07 mr1662_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
vg0204430393 NA 8.77E-07 mr1745_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
vg0204430393 NA 5.93E-06 mr1908_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