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Detailed information for vg0720451131:

Variant ID: vg0720451131 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20451131
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTAAAAATGTACTCCCTCCGTCCCACTCAATAACGCAGTCGAAAATGGCACGGTCTCCAAAATTAATATTTGACTTTAAATTTTTCATATAATATAAT[G/A]
TTTGTAACAACAAAATCATAACCATATGAAAATAAATTAAAATATAAATTGATCAATTCATTGATAGTGTTTTCATCAAATAAAATTTATTTTAGAATAA

Reverse complement sequence

TTATTCTAAAATAAATTTTATTTGATGAAAACACTATCAATGAATTGATCAATTTATATTTTAATTTATTTTCATATGGTTATGATTTTGTTGTTACAAA[C/T]
ATTATATTATATGAAAAATTTAAAGTCAAATATTAATTTTGGAGACCGTGCCATTTTCGACTGCGTTATTGAGTGGGACGGAGGGAGTACATTTTTAGAA

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 87.70% 12.20% 0.08% 0.00% NA
All Indica  2759 91.70% 8.30% 0.04% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 8.90% 90.70% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 83.00% 16.80% 0.22% 0.00% NA
Indica III  913 91.50% 8.50% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 9.20% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 83.30% 2.08% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0720451131 G -> A LOC_Os07g34180.1 upstream_gene_variant ; 1767.0bp to feature; MODIFIER silent_mutation Average:44.491; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0720451131 G -> A LOC_Os07g34170.1 downstream_gene_variant ; 787.0bp to feature; MODIFIER silent_mutation Average:44.491; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0720451131 G -> A LOC_Os07g34190.1 downstream_gene_variant ; 4381.0bp to feature; MODIFIER silent_mutation Average:44.491; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0720451131 G -> A LOC_Os07g34170-LOC_Os07g34180 intergenic_region ; MODIFIER silent_mutation Average:44.491; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720451131 NA 2.85E-07 mr1193 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
vg0720451131 8.33E-06 3.24E-07 mr1705 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
vg0720451131 NA 7.76E-06 mr1808 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