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Detailed information for vg0204918488:

Variant ID: vg0204918488 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4918488
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, T: 0.24, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


GCATTCATTACCCCCATAGGAACTTATTGTTATACGACAATGCCTTTCGGGTTAAAGAATGCAGGTCCTACTTTTCAACGTACTACTCGAATTTCTTTGG[T/G]
TAGCCAAATAGGACGTAATGTTGAGGCCTATGTTGATGACTTGGTTGTGAAAACACGCAACCAGGAGACCTTACTCTCGGATCTAGCGGAAACTTTCGAA

Reverse complement sequence

TTCGAAAGTTTCCGCTAGATCCGAGAGTAAGGTCTCCTGGTTGCGTGTTTTCACAACCAAGTCATCAACATAGGCCTCAACATTACGTCCTATTTGGCTA[A/C]
CCAAAGAAATTCGAGTAGTACGTTGAAAAGTAGGACCTGCATTCTTTAACCCGAAAGGCATTGTCGTATAACAATAAGTTCCTATGGGGGTAATGAATGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.90% 20.80% 6.62% 30.66% NA
All Indica  2759 48.50% 1.20% 10.69% 39.65% NA
All Japonica  1512 38.00% 61.20% 0.07% 0.73% NA
Aus  269 9.30% 0.00% 3.35% 87.36% NA
Indica I  595 62.70% 1.20% 5.71% 30.42% NA
Indica II  465 46.20% 1.70% 6.24% 45.81% NA
Indica III  913 36.80% 0.30% 17.42% 45.45% NA
Indica Intermediate  786 52.70% 1.80% 9.29% 36.26% NA
Temperate Japonica  767 6.50% 93.00% 0.13% 0.39% NA
Tropical Japonica  504 90.90% 8.50% 0.00% 0.60% NA
Japonica Intermediate  241 27.40% 70.50% 0.00% 2.07% NA
VI/Aromatic  96 8.30% 1.00% 4.17% 86.46% NA
Intermediate  90 41.10% 25.60% 4.44% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204918488 T -> G LOC_Os02g09550.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:10.596; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 N N N N
vg0204918488 T -> G LOC_Os02g09560.1 downstream_gene_variant ; 3607.0bp to feature; MODIFIER silent_mutation Average:10.596; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 N N N N
vg0204918488 T -> DEL N N silent_mutation Average:10.596; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204918488 NA 5.68E-07 mr1252 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
vg0204918488 NA 4.98E-07 mr1252 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
vg0204918488 NA 5.48E-07 mr1543 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
vg0204918488 NA 2.91E-06 mr1602 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
vg0204918488 NA 1.47E-06 mr1682 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
vg0204918488 NA 1.51E-29 mr1789 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
vg0204918488 NA 2.65E-06 mr1815 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
vg0204918488 NA 2.16E-09 mr1011_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
vg0204918488 NA 4.37E-07 mr1401_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
vg0204918488 3.27E-06 5.57E-21 mr1682_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
vg0204918488 NA 4.02E-06 mr1682_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
vg0204918488 NA 1.69E-30 mr1789_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
vg0204918488 NA 6.83E-11 mr1789_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