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Detailed information for vg0220950949:

Variant ID: vg0220950949 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20950949
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GGTAAGTAGTCATCTGTGACGGGCTCTAGTTTAGACCCGATTGAGATGAGTATCATCTGTGATGTGCTCTAGTGTAGGCCCGATTGAGGTTAGTAGTCAT[C/T]
TGTGACGGGCGCTAGTTGTGGCCCGATTGAGATAGGTCATCTGTGATGGGCTATAGTTTGACTGGTCGTCTGGGTCAAAGCTATCGGTGGCGGGTTCATC

Reverse complement sequence

GATGAACCCGCCACCGATAGCTTTGACCCAGACGACCAGTCAAACTATAGCCCATCACAGATGACCTATCTCAATCGGGCCACAACTAGCGCCCGTCACA[G/A]
ATGACTACTAACCTCAATCGGGCCTACACTAGAGCACATCACAGATGATACTCATCTCAATCGGGTCTAAACTAGAGCCCGTCACAGATGACTACTTACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.80% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 92.90% 7.10% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0220950949 C -> T LOC_Os02g34910.1 upstream_gene_variant ; 2858.0bp to feature; MODIFIER silent_mutation Average:56.555; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0220950949 C -> T LOC_Os02g34930.1 upstream_gene_variant ; 4270.0bp to feature; MODIFIER silent_mutation Average:56.555; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0220950949 C -> T LOC_Os02g34900.1 downstream_gene_variant ; 4717.0bp to feature; MODIFIER silent_mutation Average:56.555; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0220950949 C -> T LOC_Os02g34920.1 intron_variant ; MODIFIER silent_mutation Average:56.555; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220950949 NA 1.43E-06 mr1069 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
vg0220950949 NA 1.90E-06 mr1101 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
vg0220950949 4.60E-06 5.51E-07 mr1150 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
vg0220950949 8.26E-07 8.26E-07 mr1200 Jap_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
vg0220950949 NA 1.16E-06 mr1441 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
vg0220950949 2.30E-06 2.30E-06 mr1861 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