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Detailed information for vg0224190332:

Variant ID: vg0224190332 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24190332
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTAATCCTCAATTAATAAATGCATTTAATAATCAAATTCGGCGTGGTGGAATTTTTCTTGAGTTCCCCATGCTCCAATACATTAACAAGACTTTTAGTG[C/G]
AATTTTCAGAGCTCTCGAAATAATTTTAACCAATTAAAATTGAGCACATGCAATTTTTAAATCCCAGGGAAAATCTTTTCCTCCTTTTCTTTTTCTTTTC

Reverse complement sequence

GAAAAGAAAAAGAAAAGGAGGAAAAGATTTTCCCTGGGATTTAAAAATTGCATGTGCTCAATTTTAATTGGTTAAAATTATTTCGAGAGCTCTGAAAATT[G/C]
CACTAAAAGTCTTGTTAATGTATTGGAGCATGGGGAACTCAAGAAAAATTCCACCACGCCGAATTTGATTATTAAATGCATTTATTAATTGAGGATTAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 10.50% 2.05% 34.62% NA
All Indica  2759 39.00% 5.50% 3.23% 52.34% NA
All Japonica  1512 78.10% 18.00% 0.13% 3.77% NA
Aus  269 49.40% 11.50% 1.49% 37.55% NA
Indica I  595 39.20% 1.00% 2.18% 57.65% NA
Indica II  465 51.20% 4.50% 1.08% 43.23% NA
Indica III  913 22.60% 7.60% 5.37% 64.51% NA
Indica Intermediate  786 50.60% 7.00% 2.80% 39.57% NA
Temperate Japonica  767 80.40% 17.50% 0.26% 1.83% NA
Tropical Japonica  504 81.20% 11.10% 0.00% 7.74% NA
Japonica Intermediate  241 64.30% 34.00% 0.00% 1.66% NA
VI/Aromatic  96 51.00% 36.50% 1.04% 11.46% NA
Intermediate  90 66.70% 6.70% 1.11% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0224190332 C -> G LOC_Os02g39990-LOC_Os02g40000 intergenic_region ; MODIFIER silent_mutation Average:51.971; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0224190332 C -> DEL N N silent_mutation Average:51.971; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224190332 4.42E-06 NA mr1101 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
vg0224190332 7.20E-06 NA mr1101 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
vg0224190332 3.03E-06 NA mr1098_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
vg0224190332 3.34E-06 NA mr1098_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
vg0224190332 1.82E-06 NA mr1099_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
vg0224190332 1.26E-06 NA mr1123_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
vg0224190332 2.83E-06 9.05E-06 mr1123_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
vg0224190332 3.67E-06 NA mr1150_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
vg0224190332 2.96E-06 NA mr1936_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