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Detailed information for vg0103668168:

Variant ID: vg0103668168 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3668168
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACCTGGAACAAAAACTCAAGTTATCAGAAATGCTGCTCATGATAACCGCCTTTAAGAACAAATTATACCCTTTATCAGTCCTTTTAGATCTCAACTG[G/A]
TTTGAAAAGAATATGCTAAATTATGGTGGATGTCCACACTAGATAAATAGAGATAGATATGCATCTAGTTTCTCAAGAACATTTTTTCAGCTTATCTGTT

Reverse complement sequence

AACAGATAAGCTGAAAAAATGTTCTTGAGAAACTAGATGCATATCTATCTCTATTTATCTAGTGTGGACATCCACCATAATTTAGCATATTCTTTTCAAA[C/T]
CAGTTGAGATCTAAAAGGACTGATAAAGGGTATAATTTGTTCTTAAAGGCGGTTATCATGAGCAGCATTTCTGATAACTTGAGTTTTTGTTCCAGGTAAA

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 66.10% 33.80% 0.08% 0.00% NA
All Indica  2759 95.50% 4.50% 0.00% 0.00% NA
All Japonica  1512 24.10% 75.70% 0.20% 0.00% NA
Aus  269 14.10% 85.90% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 93.00% 7.00% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.90% 0.00% 0.00% NA
Temperate Japonica  767 6.40% 93.40% 0.26% 0.00% NA
Tropical Japonica  504 54.60% 45.40% 0.00% 0.00% NA
Japonica Intermediate  241 16.60% 83.00% 0.41% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 1.11% 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
vg0103668168 G -> A LOC_Os01g07620.1 upstream_gene_variant ; 2122.0bp to feature; MODIFIER silent_mutation Average:53.108; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0103668168 G -> A LOC_Os01g07610.1 downstream_gene_variant ; 3849.0bp to feature; MODIFIER silent_mutation Average:53.108; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0103668168 G -> A LOC_Os01g07630.1 intron_variant ; MODIFIER silent_mutation Average:53.108; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103668168 NA 9.60E-07 mr1925 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
vg0103668168 NA 4.69E-12 mr1228_2 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
vg0103668168 NA 1.79E-23 mr1401_2 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
vg0103668168 NA 4.07E-07 mr1446_2 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
vg0103668168 NA 9.32E-06 mr1869_2 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