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Detailed information for vg0313149395:

Variant ID: vg0313149395 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13149395
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTATTTTTATAAAAAATTATAGTGCACTTACATATCATATCAACTGAATTTACAAATGTAATTTTAGTTATGTAGGACTGTAATTTTATATTTTAAAAT[A/G]
TAATTTTAGTTATATAAGACTGTAATTTTATTTTTTTTAAAAAAATAACAAATACATATTTACTTATACCAAAATTACAGTGCACTTACATGTCATATCA

Reverse complement sequence

TGATATGACATGTAAGTGCACTGTAATTTTGGTATAAGTAAATATGTATTTGTTATTTTTTTAAAAAAAATAAAATTACAGTCTTATATAACTAAAATTA[T/C]
ATTTTAAAATATAAAATTACAGTCCTACATAACTAAAATTACATTTGTAAATTCAGTTGATATGATATGTAAGTGCACTATAATTTTTTATAAAAATAAT

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 88.80% 9.60% 1.54% 0.00% NA
All Indica  2759 98.20% 0.10% 1.70% 0.00% NA
All Japonica  1512 70.20% 28.40% 1.32% 0.00% NA
Aus  269 91.80% 6.30% 1.86% 0.00% NA
Indica I  595 98.00% 0.00% 2.02% 0.00% NA
Indica II  465 96.10% 0.00% 3.87% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 97.70% 0.30% 2.04% 0.00% NA
Temperate Japonica  767 57.60% 40.20% 2.22% 0.00% NA
Tropical Japonica  504 89.90% 9.90% 0.20% 0.00% NA
Japonica Intermediate  241 69.30% 29.90% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0313149395 A -> G LOC_Os03g22770.1 upstream_gene_variant ; 3565.0bp to feature; MODIFIER silent_mutation Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0313149395 A -> G LOC_Os03g22770.2 upstream_gene_variant ; 3565.0bp to feature; MODIFIER silent_mutation Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0313149395 A -> G LOC_Os03g22760.1 downstream_gene_variant ; 287.0bp to feature; MODIFIER silent_mutation Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N
vg0313149395 A -> G LOC_Os03g22760-LOC_Os03g22770 intergenic_region ; MODIFIER silent_mutation Average:35.538; most accessible tissue: Zhenshan97 flag leaf, score: 58.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313149395 NA 2.81E-06 mr1530 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
vg0313149395 NA 7.35E-09 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
vg0313149395 4.78E-06 NA mr1530_2 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