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Detailed information for vg0336051407:

Variant ID: vg0336051407 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36051407
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGCGCGTAACGGATCCAGAAATCTCCGGCGGGCATCTCTCCCCTTTCCTTGGAAGTCGTACCGTCGGAAGTGTGTCTATTTAAAGGAATTTTGGGGAT[C/T]
CATTTTGAAGTCCGCCTATTGTGAAGAAAACATCCCGCCTGTAAGCGCTCTTCGTCTTCTCCGCTGCCACAAGAAACCCTAGTTCATCGACCTGAGCCCT

Reverse complement sequence

AGGGCTCAGGTCGATGAACTAGGGTTTCTTGTGGCAGCGGAGAAGACGAAGAGCGCTTACAGGCGGGATGTTTTCTTCACAATAGGCGGACTTCAAAATG[G/A]
ATCCCCAAAATTCCTTTAAATAGACACACTTCCGACGGTACGACTTCCAAGGAAAGGGGAGAGATGCCCGCCGGAGATTTCTGGATCCGTTACGCGCGGC

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 94.90% 5.10% 0.04% 0.00% NA
All Indica  2759 91.30% 8.60% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 95.50% 4.50% 0.00% 0.00% NA
Indica III  913 85.00% 14.90% 0.11% 0.00% NA
Indica Intermediate  786 92.20% 7.60% 0.13% 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 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
vg0336051407 C -> T LOC_Os03g63820.1 upstream_gene_variant ; 125.0bp to feature; MODIFIER silent_mutation Average:36.602; most accessible tissue: Zhenshan97 flower, score: 52.192 N N N N
vg0336051407 C -> T LOC_Os03g63830.1 downstream_gene_variant ; 4424.0bp to feature; MODIFIER silent_mutation Average:36.602; most accessible tissue: Zhenshan97 flower, score: 52.192 N N N N
vg0336051407 C -> T LOC_Os03g63810-LOC_Os03g63820 intergenic_region ; MODIFIER silent_mutation Average:36.602; most accessible tissue: Zhenshan97 flower, score: 52.192 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0336051407 NA 9.38E-06 mr1165 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
vg0336051407 4.02E-06 5.08E-06 mr1479 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
vg0336051407 NA 1.06E-06 mr1522 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
vg0336051407 3.44E-06 1.33E-07 mr1553 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
vg0336051407 1.65E-07 1.78E-07 mr1892 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