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Detailed information for vg0322439061:

Variant ID: vg0322439061 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22439061
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAATTGGACAATATCAAATATGTTTATTTTTTGGGAGCATGTATATTGTACCTGATTGGAGCCGGCCTATGTAACCTGACGAATGAGTTTGAACCGGCAA[C/T]
GGCGCTTCCAATGGAAGGGGAGGTTGGCCACGACGAGGCTGTGTCCCTGACCGGACGGCGATAAGGCTTTGCTTGATACCGTGACAGGAATCAGGGAATG

Reverse complement sequence

CATTCCCTGATTCCTGTCACGGTATCAAGCAAAGCCTTATCGCCGTCCGGTCAGGGACACAGCCTCGTCGTGGCCAACCTCCCCTTCCATTGGAAGCGCC[G/A]
TTGCCGGTTCAAACTCATTCGTCAGGTTACATAGGCCGGCTCCAATCAGGTACAATATACATGCTCCCAAAAAATAAACATATTTGATATTGTCCAATTG

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 98.70% 0.30% 0.95% 0.00% NA
All Indica  2759 97.80% 0.60% 1.59% 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 92.80% 1.80% 5.38% 0.00% NA
Indica II  465 99.10% 0.20% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 0.50% 1.15% 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 98.90% 0.00% 1.11% 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
vg0322439061 C -> T LOC_Os03g40370.1 upstream_gene_variant ; 2951.0bp to feature; MODIFIER silent_mutation Average:54.017; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N
vg0322439061 C -> T LOC_Os03g40380.1 upstream_gene_variant ; 2099.0bp to feature; MODIFIER silent_mutation Average:54.017; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N
vg0322439061 C -> T LOC_Os03g40390.1 upstream_gene_variant ; 4212.0bp to feature; MODIFIER silent_mutation Average:54.017; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N
vg0322439061 C -> T LOC_Os03g40370-LOC_Os03g40380 intergenic_region ; MODIFIER silent_mutation Average:54.017; most accessible tissue: Zhenshan97 flower, score: 76.324 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322439061 NA 8.05E-06 mr1734 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
vg0322439061 5.13E-06 NA mr1669_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
vg0322439061 1.29E-06 4.62E-06 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