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Detailed information for vg0218086395:

Variant ID: vg0218086395 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18086395
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCACCTCCGATTTGTATATAATCACCAAAATAAATTCACTATAAATTTTGGCATGACCTCCCCTCTTTTTTGAAGAAATTTTGAAGCTTGCTCGGGCAG[C/T]
TGGAGGAGGAAGAAGACATATATATAGGGGTGGGACTTTAGTCCCGGTTGACTAAAGTTACGATCTTTAGTCCCGGTTGGTGTGATCCCGGGGGGCTTGA

Reverse complement sequence

TCAAGCCCCCCGGGATCACACCAACCGGGACTAAAGATCGTAACTTTAGTCAACCGGGACTAAAGTCCCACCCCTATATATATGTCTTCTTCCTCCTCCA[G/A]
CTGCCCGAGCAAGCTTCAAAATTTCTTCAAAAAAGAGGGGAGGTCATGCCAAAATTTATAGTGAATTTATTTTGGTGATTATATACAAATCGGAGGTGCC

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 79.10% 20.70% 0.17% 0.00% NA
All Indica  2759 66.30% 33.40% 0.29% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 79.20% 20.50% 0.34% 0.00% NA
Indica II  465 89.00% 11.00% 0.00% 0.00% NA
Indica III  913 37.20% 62.30% 0.44% 0.00% NA
Indica Intermediate  786 76.80% 22.90% 0.25% 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 90.00% 10.00% 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
vg0218086395 C -> T LOC_Os02g30360.1 upstream_gene_variant ; 2173.0bp to feature; MODIFIER silent_mutation Average:33.454; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0218086395 C -> T LOC_Os02g30370.1 intron_variant ; MODIFIER silent_mutation Average:33.454; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218086395 1.76E-06 NA mr1310 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