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Detailed information for vg0620635407:

Variant ID: vg0620635407 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20635407
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGCAAATTGCAATGTAGCTAGATATGTAGCATGAACAATATTTCAGACACATAATTTTGAATTGCACCTTTTTCAAATCTGTTTGTTACAATCTAAAA[A/C]
CAGCCTGTAAAAAAAATTCAAAATTTGATCATTTAAACCTGCCGTGTATCCTAGAGCTATTAAAAGGTTAAAACGACCCGAAAAACCTATAGAAAATTAG

Reverse complement sequence

CTAATTTTCTATAGGTTTTTCGGGTCGTTTTAACCTTTTAATAGCTCTAGGATACACGGCAGGTTTAAATGATCAAATTTTGAATTTTTTTTACAGGCTG[T/G]
TTTTAGATTGTAACAAACAGATTTGAAAAAGGTGCAATTCAAAATTATGTGTCTGAAATATTGTTCATGCTACATATCTAGCTACATTGCAATTTGCAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.50% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.40% 4.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.90% 5.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0620635407 A -> C LOC_Os06g35410.1 3_prime_UTR_variant ; 168.0bp to feature; MODIFIER silent_mutation Average:66.704; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N
vg0620635407 A -> C LOC_Os06g35400.1 downstream_gene_variant ; 2993.0bp to feature; MODIFIER silent_mutation Average:66.704; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620635407 6.55E-07 6.55E-07 mr1024_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
vg0620635407 NA 2.78E-06 mr1565_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
vg0620635407 NA 9.33E-06 mr1827_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
vg0620635407 2.74E-06 2.74E-06 mr1915_2 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