Search for Variation information by Variation ID:

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

Detailed information for vg0328706766:

Variant ID: vg0328706766 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28706766
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGCATAAAGCCCCTCGCCGAGCCACTTCTTTGACAATACATCATGATGAATAGGGTTCGACTCATTCATGTCTCCACACCCAGGTTGTGCCGCAGCCGC[C/T]
CTTCTGCCCGCAGCCCTATTCTATAAATTTGGCTGGCTACGTTACTTATAATCGCAGAACGAGCAATGAATCCCCAACGACAAACGAACAAGGGGCGAGG

Reverse complement sequence

CCTCGCCCCTTGTTCGTTTGTCGTTGGGGATTCATTGCTCGTTCTGCGATTATAAGTAACGTAGCCAGCCAAATTTATAGAATAGGGCTGCGGGCAGAAG[G/A]
GCGGCTGCGGCACAACCTGGGTGTGGAGACATGAATGAGTCGAACCCTATTCATCATGATGTATTGTCAAAGAAGTGGCTCGGCGAGGGGCTTTATGCTG

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 97.10% 2.10% 0.78% 0.00% NA
All Indica  2759 95.10% 3.60% 1.30% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.40% 11.60% 5.04% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 2.90% 0.76% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 97.80% 2.20% 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
vg0328706766 C -> T LOC_Os03g50325.1 upstream_gene_variant ; 1273.0bp to feature; MODIFIER silent_mutation Average:55.252; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0328706766 C -> T LOC_Os03g50330.1 downstream_gene_variant ; 1819.0bp to feature; MODIFIER silent_mutation Average:55.252; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0328706766 C -> T LOC_Os03g50325-LOC_Os03g50330 intergenic_region ; MODIFIER silent_mutation Average:55.252; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328706766 NA 1.11E-11 mr1038 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
vg0328706766 NA 2.78E-13 mr1389 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
vg0328706766 1.29E-09 6.74E-22 mr1038_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
vg0328706766 NA 1.30E-11 mr1141_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
vg0328706766 3.44E-09 1.01E-21 mr1389_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
vg0328706766 NA 9.80E-06 mr1521_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