Search for Variation information by Variation ID:

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

Detailed information for vg0335773756:

Variant ID: vg0335773756 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35773756
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTCCAGTGGATAGATTTGCTGTACTGCCAGGAGAAGACAGAGAAACTGACTAATACAAACATCATTGATCACTGACCCAAAAAAAAAAAAAACTTTATTC[T/C]
TTTTCTTCATCAAGTCCATGTCTACTATTAGAATGTTGAATTATGAATTTTACCCTCGAGCTAACATATGTAGCCCTATCACCCAATATTTACACATTAC

Reverse complement sequence

GTAATGTGTAAATATTGGGTGATAGGGCTACATATGTTAGCTCGAGGGTAAAATTCATAATTCAACATTCTAATAGTAGACATGGACTTGATGAAGAAAA[A/G]
GAATAAAGTTTTTTTTTTTTTTGGGTCAGTGATCAATGATGTTTGTATTAGTCAGTTTCTCTGTCTTCTCCTGGCAGTACAGCAAATCTATCCACTGGAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.50% 0.04% 0.00% NA
All Indica  2759 90.90% 9.00% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 88.40% 11.50% 0.11% 0.00% NA
Indica Intermediate  786 90.10% 9.80% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0335773756 T -> C LOC_Os03g63290.1 upstream_gene_variant ; 1509.0bp to feature; MODIFIER silent_mutation Average:39.108; most accessible tissue: Callus, score: 67.815 N N N N
vg0335773756 T -> C LOC_Os03g63310.1 upstream_gene_variant ; 4153.0bp to feature; MODIFIER silent_mutation Average:39.108; most accessible tissue: Callus, score: 67.815 N N N N
vg0335773756 T -> C LOC_Os03g63280.1 downstream_gene_variant ; 4663.0bp to feature; MODIFIER silent_mutation Average:39.108; most accessible tissue: Callus, score: 67.815 N N N N
vg0335773756 T -> C LOC_Os03g63300.1 intron_variant ; MODIFIER silent_mutation Average:39.108; most accessible tissue: Callus, score: 67.815 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335773756 8.42E-06 8.42E-06 mr1978 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