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Detailed information for vg0218865603:

Variant ID: vg0218865603 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18865603
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAACAGAGGAGGAGGAACTCGAAGTGCAAGAGTCGTGAAGAACTTCGTCCGTCCTTCTGCTCGCTGTGGAGTATATATATGCGAGCGCAAGAGTAACGTT[C/T]
GGAGTCATCAACCGCGGTGTTTAATTTCGTAACCGACACGCTCGTTAATATGGAATCAATTCACGGCGTTTAATTCCGTAACCGACGGAATCAATTCACG

Reverse complement sequence

CGTGAATTGATTCCGTCGGTTACGGAATTAAACGCCGTGAATTGATTCCATATTAACGAGCGTGTCGGTTACGAAATTAAACACCGCGGTTGATGACTCC[G/A]
AACGTTACTCTTGCGCTCGCATATATATACTCCACAGCGAGCAGAAGGACGGACGAAGTTCTTCACGACTCTTGCACTTCGAGTTCCTCCTCCTCTGTTC

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 89.10% 10.90% 0.00% 0.00% NA
All Indica  2759 84.70% 15.30% 0.00% 0.00% NA
All Japonica  1512 95.80% 4.20% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 70.30% 29.70% 0.00% 0.00% NA
Indica Intermediate  786 84.20% 15.80% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 93.80% 6.20% 0.00% 0.00% NA
Japonica Intermediate  241 88.00% 12.00% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0218865603 C -> T LOC_Os02g31922.1 downstream_gene_variant ; 4615.0bp to feature; MODIFIER silent_mutation Average:48.25; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0218865603 C -> T LOC_Os02g31924.1 downstream_gene_variant ; 3598.0bp to feature; MODIFIER silent_mutation Average:48.25; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0218865603 C -> T LOC_Os02g31926.1 downstream_gene_variant ; 2400.0bp to feature; MODIFIER silent_mutation Average:48.25; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0218865603 C -> T LOC_Os02g31926-LOC_Os02g31940 intergenic_region ; MODIFIER silent_mutation Average:48.25; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218865603 6.79E-07 6.79E-07 mr1275 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