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Detailed information for vg0816379648:

Variant ID: vg0816379648 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16379648
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


GGTCATTGGTGCATGTCATACAACCGACACCTTTGTGCTCTCTCGATTCAAAAAAGAAGAAGTCGGCTCCAAGCCGAGCCGAGCCAAAATCAAATCCATC[A/T]
AATATCACAACAATGACATCAATAATCCCTAATCCAATCTATCACCAATCATAGATGAACAACAATCCTATCTAGTTTGTATGATATCAACAAATATATG

Reverse complement sequence

CATATATTTGTTGATATCATACAAACTAGATAGGATTGTTGTTCATCTATGATTGGTGATAGATTGGATTAGGGATTATTGATGTCATTGTTGTGATATT[T/A]
GATGGATTTGATTTTGGCTCGGCTCGGCTTGGAGCCGACTTCTTCTTTTTTGAATCGAGAGAGCACAAAGGTGTCGGTTGTATGACATGCACCAATGACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.10% 43.80% 0.08% 0.00% NA
All Indica  2759 26.50% 73.40% 0.14% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 33.90% 66.10% 0.00% 0.00% NA
Indica II  465 9.20% 90.80% 0.00% 0.00% NA
Indica III  913 32.50% 67.40% 0.11% 0.00% NA
Indica Intermediate  786 23.90% 75.70% 0.38% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0816379648 A -> T LOC_Os08g26880-LOC_Os08g26890 intergenic_region ; MODIFIER silent_mutation Average:39.665; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816379648 NA 2.99E-07 mr1321 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
vg0816379648 1.81E-06 1.61E-06 mr1349 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
vg0816379648 NA 7.91E-11 mr1581 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