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Detailed information for vg0816447256:

Variant ID: vg0816447256 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16447256
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATATTTCAGTAATTACCCACATATTAAATTAATCATTAAATGGTCTAATTATAATTTTTTAAGTACTTTGAGTGTCCAAGTATTTTAAGGATTTTTCTT[G/A]
AAATTATTTGAGCATTGGAAGTATTTTTAACAATTCAAAATCATTTAAGTGATTATTTTAATTGGAAAAGTAATAAAATTCTCCTCCCTTGTCTTAGGCT

Reverse complement sequence

AGCCTAAGACAAGGGAGGAGAATTTTATTACTTTTCCAATTAAAATAATCACTTAAATGATTTTGAATTGTTAAAAATACTTCCAATGCTCAAATAATTT[C/T]
AAGAAAAATCCTTAAAATACTTGGACACTCAAAGTACTTAAAAAATTATAATTAGACCATTTAATGATTAATTTAATATGTGGGTAATTACTGAAATATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.02% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 94.00% 5.90% 0.07% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 95.70% 4.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 84.10% 15.70% 0.20% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 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
vg0816447256 G -> A LOC_Os08g26940.1 upstream_gene_variant ; 2927.0bp to feature; MODIFIER silent_mutation Average:52.949; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N
vg0816447256 G -> A LOC_Os08g26950.1 upstream_gene_variant ; 4822.0bp to feature; MODIFIER silent_mutation Average:52.949; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N
vg0816447256 G -> A LOC_Os08g26940-LOC_Os08g26950 intergenic_region ; MODIFIER silent_mutation Average:52.949; most accessible tissue: Zhenshan97 flower, score: 81.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816447256 1.33E-06 5.30E-10 mr1076 Jap_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
vg0816447256 NA 6.61E-09 mr1082 Jap_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
vg0816447256 2.78E-06 2.09E-09 mr1083 Jap_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
vg0816447256 NA 1.35E-06 mr1086 Jap_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
vg0816447256 NA 8.42E-06 mr1103 Jap_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
vg0816447256 NA 3.56E-08 mr1226 Jap_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
vg0816447256 1.97E-08 9.72E-12 mr1227 Jap_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
vg0816447256 NA 7.52E-07 mr1408 Jap_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
vg0816447256 1.08E-07 1.04E-09 mr1411 Jap_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
vg0816447256 NA 2.58E-08 mr1560 Jap_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
vg0816447256 NA 6.56E-06 mr1082_2 Jap_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
vg0816447256 NA 1.32E-06 mr1226_2 Jap_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