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Detailed information for vg0316601740:

Variant ID: vg0316601740 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16601740
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AGGCACGGGCAGATCAGAACAAATTCTGCATTGCAACAGTCAAATGCTGCCAACAAACCGAAAATGATTCTTCCTGCAATTCTGCATAAAAATGGCAAAA[A/G]
AATAATGATAAAAATCATAACCAAACCAGCAATATACAACTAAAAAATATAGATGCTACAATATGGACTATTGCAAATGAGAGACGAACCTTCTCCACCT

Reverse complement sequence

AGGTGGAGAAGGTTCGTCTCTCATTTGCAATAGTCCATATTGTAGCATCTATATTTTTTAGTTGTATATTGCTGGTTTGGTTATGATTTTTATCATTATT[T/C]
TTTTGCCATTTTTATGCAGAATTGCAGGAAGAATCATTTTCGGTTTGTTGGCAGCATTTGACTGTTGCAATGCAGAATTTGTTCTGATCTGCCCGTGCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 91.50% 8.50% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 94.30% 5.70% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 86.90% 13.10% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 9.20% 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 94.40% 5.60% 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
vg0316601740 A -> G LOC_Os03g29200.1 upstream_gene_variant ; 1703.0bp to feature; MODIFIER silent_mutation Average:58.183; most accessible tissue: Callus, score: 90.667 N N N N
vg0316601740 A -> G LOC_Os03g29206.1 upstream_gene_variant ; 3926.0bp to feature; MODIFIER silent_mutation Average:58.183; most accessible tissue: Callus, score: 90.667 N N N N
vg0316601740 A -> G LOC_Os03g29194.1 intron_variant ; MODIFIER silent_mutation Average:58.183; most accessible tissue: Callus, score: 90.667 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316601740 3.85E-06 3.61E-06 mr1119 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
vg0316601740 NA 7.50E-06 mr1515 Ind_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
vg0316601740 NA 6.10E-06 mr1917 Ind_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