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Detailed information for vg0621384427:

Variant ID: vg0621384427 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21384427
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGCAGTAGCAGTTAGAAGCTCCCCAAACAGACTCAAAAGGTCTTATATATTTGGACACTTATAAAAGTCAGACACTTACAAAAGTCAACTCCAGATAAA[C/G]
GAGAAACACTACGGGGCGGACGTAGGTTTGAGGCCACATGGATTAATGACCGTACTGAATGAGCAAGGCGGCATTGAAAGAATAAATACTTGATTGCCTC

Reverse complement sequence

GAGGCAATCAAGTATTTATTCTTTCAATGCCGCCTTGCTCATTCAGTACGGTCATTAATCCATGTGGCCTCAAACCTACGTCCGCCCCGTAGTGTTTCTC[G/C]
TTTATCTGGAGTTGACTTTTGTAAGTGTCTGACTTTTATAAGTGTCCAAATATATAAGACCTTTTGAGTCTGTTTGGGGAGCTTCTAACTGCTACTGCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.80% 6.90% 0.32% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 0.00% NA
All Japonica  1512 80.40% 18.90% 0.73% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 97.10% 1.80% 1.04% 0.00% NA
Tropical Japonica  504 49.80% 49.60% 0.60% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 19.80% 1.04% 0.00% NA
Intermediate  90 85.60% 12.20% 2.22% 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
vg0621384427 C -> G LOC_Os06g36420.1 downstream_gene_variant ; 1559.0bp to feature; MODIFIER silent_mutation Average:44.087; most accessible tissue: Callus, score: 83.378 N N N N
vg0621384427 C -> G LOC_Os06g36410-LOC_Os06g36420 intergenic_region ; MODIFIER silent_mutation Average:44.087; most accessible tissue: Callus, score: 83.378 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621384427 NA 4.24E-11 mr1235 Jap_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
vg0621384427 NA 1.38E-09 mr1243 Jap_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
vg0621384427 NA 2.62E-06 mr1248 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
vg0621384427 NA 9.22E-09 mr1248 Jap_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
vg0621384427 NA 4.65E-08 mr1423 Jap_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
vg0621384427 NA 3.32E-06 mr1553_2 Jap_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