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Detailed information for vg0322405319:

Variant ID: vg0322405319 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22405319
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTACCGTGAATTGTGTCTAGCCCGCTGGTTTAGCCGCAGTCATTGTTGAGTCGTTCCCTCGTTCGTTCGAACGAGGTGTCCTCCGTGGATCGTTCGTT[C/T]
GTCCGTGTTGAGTCGTTCTTTAGTTTAGAGCCGTTCAGAGCCGCCGGTTCCGTTCACCGGTTTCGGTTGATCATTTGGGTGATCTCGTGTCATGTGAAAT

Reverse complement sequence

ATTTCACATGACACGAGATCACCCAAATGATCAACCGAAACCGGTGAACGGAACCGGCGGCTCTGAACGGCTCTAAACTAAAGAACGACTCAACACGGAC[G/A]
AACGAACGATCCACGGAGGACACCTCGTTCGAACGAACGAGGGAACGACTCAACAATGACTGCGGCTAAACCAGCGGGCTAGACACAATTCACGGTAAAG

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 98.60% 0.70% 0.63% 0.00% NA
All Indica  2759 97.60% 1.30% 1.09% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.30% 5.50% 3.19% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 0.30% 1.40% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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  90 100.00% 0.00% 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
vg0322405319 C -> T LOC_Os03g40290.1 upstream_gene_variant ; 4725.0bp to feature; MODIFIER silent_mutation Average:54.259; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N
vg0322405319 C -> T LOC_Os03g40300.1 downstream_gene_variant ; 2155.0bp to feature; MODIFIER silent_mutation Average:54.259; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N
vg0322405319 C -> T LOC_Os03g40300-LOC_Os03g40310 intergenic_region ; MODIFIER silent_mutation Average:54.259; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322405319 NA 6.50E-08 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
vg0322405319 NA 2.91E-07 mr1389_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
vg0322405319 2.45E-06 2.96E-07 mr1669_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
vg0322405319 NA 2.04E-06 mr1864_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