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Detailed information for vg0521180478:

Variant ID: vg0521180478 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21180478
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAGCAATCTTCGCCTGCGATCAAGCGAAGCTGAGCGTCGTAACCAGCCGACGGGGCCAAAGCCAGACGCTACGGAAGAGCTAGCACAGGGGGCCCCGGG[C/T]
GTCGACGGCGTCCAGAGCTCGACGCAGGGCTAGGATAGAGCTAGGAATCGTAGCCCCCACACTTTTAGCAAAGAATTGCTTGTATGAATGAAGCAAACAC

Reverse complement sequence

GTGTTTGCTTCATTCATACAAGCAATTCTTTGCTAAAAGTGTGGGGGCTACGATTCCTAGCTCTATCCTAGCCCTGCGTCGAGCTCTGGACGCCGTCGAC[G/A]
CCCGGGGCCCCCTGTGCTAGCTCTTCCGTAGCGTCTGGCTTTGGCCCCGTCGGCTGGTTACGACGCTCAGCTTCGCTTGATCGCAGGCGAAGATTGCTGG

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 99.80% 0.20% 0.02% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 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
vg0521180478 C -> T LOC_Os05g35650.1 downstream_gene_variant ; 4119.0bp to feature; MODIFIER N Average:36.837; most accessible tissue: Zhenshan97 flower, score: 55.587 N N N N
vg0521180478 C -> T LOC_Os05g35650.2 intron_variant ; MODIFIER N Average:36.837; most accessible tissue: Zhenshan97 flower, score: 55.587 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0521180478 3.94E-06 3.94E-06 mr1276_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