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Detailed information for vg0305070861:

Variant ID: vg0305070861 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 5070861
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTTGTAATGATATCACTTGAGCATCAACACCTTTGTAATCCTTGGGACCTATTTCTTTCATTCAACTCAATAAAATTATTAGTCCTAATGATCCGGTT[G/A]
TCAACCTCCACATGTTGACCAACCGATCGCATGTATAAAAGGATATGAATACATGATGAGTATTAATCAACACCACAAGTGTCATATACTCAAATATTTA

Reverse complement sequence

TAAATATTTGAGTATATGACACTTGTGGTGTTGATTAATACTCATCATGTATTCATATCCTTTTATACATGCGATCGGTTGGTCAACATGTGGAGGTTGA[C/T]
AACCGGATCATTAGGACTAATAATTTTATTGAGTTGAATGAAAGAAATAGGTCCCAAGGATTACAAAGGTGTTGATGCTCAAGTGATATCATTACAACTA

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 65.20% 34.80% 0.02% 0.00% NA
All Indica  2759 98.10% 1.90% 0.04% 0.00% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 1.90% 0.13% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0305070861 G -> A LOC_Os03g10050-LOC_Os03g10060 intergenic_region ; MODIFIER silent_mutation Average:16.542; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0305070861 NA 1.66E-13 mr1010 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
vg0305070861 NA 1.21E-07 mr1162 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
vg0305070861 4.61E-06 NA mr1179 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
vg0305070861 NA 8.01E-06 mr1285 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
vg0305070861 NA 2.16E-09 mr1299 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
vg0305070861 NA 3.70E-06 mr1408 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
vg0305070861 NA 4.54E-27 mr1423 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
vg0305070861 NA 1.11E-08 mr1637 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