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Detailed information for vg0329570872:

Variant ID: vg0329570872 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29570872
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TCGTATAACCTTAGCAACCATCATACCCCGATACTCCCGAATACGTAATTCAGGATGAGAATGGTTAGGATATGGATTGAACCTAAACCGTTTTAAGTGA[G/T]
TTCGTTGATCCATGGTTTAATAGGGTCGATCCACCATGAGTCCATTATATCAATAGGTTATCCATATTACGTGTTGGTAAAACTCGGACCCAAAATTTTT

Reverse complement sequence

AAAAATTTTGGGTCCGAGTTTTACCAACACGTAATATGGATAACCTATTGATATAATGGACTCATGGTGGATCGACCCTATTAAACCATGGATCAACGAA[C/A]
TCACTTAAAACGGTTTAGGTTCAATCCATATCCTAACCATTCTCATCCTGAATTACGTATTCGGGAGTATCGGGGTATGATGGTTGCTAAGGTTATACGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.10% 13.80% 0.08% 0.00% NA
All Indica  2759 76.90% 22.90% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 64.30% 35.50% 0.22% 0.00% NA
Indica III  913 72.90% 26.90% 0.11% 0.00% NA
Indica Intermediate  786 73.70% 26.10% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0329570872 G -> T LOC_Os03g51650.1 upstream_gene_variant ; 4849.0bp to feature; MODIFIER silent_mutation Average:49.648; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N
vg0329570872 G -> T LOC_Os03g51650-LOC_Os03g51660 intergenic_region ; MODIFIER silent_mutation Average:49.648; most accessible tissue: Minghui63 panicle, score: 71.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329570872 NA 4.41E-06 mr1343 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
vg0329570872 NA 1.09E-08 mr1829 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
vg0329570872 9.98E-07 5.23E-14 mr1829 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
vg0329570872 NA 2.34E-07 mr1842 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
vg0329570872 NA 1.34E-07 mr1902 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
vg0329570872 NA 7.26E-11 mr1829_2 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