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Detailed information for vg0319749387:

Variant ID: vg0319749387 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19749387
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATGTGGGGTGCAACCCAATCTGGTGTAGCATGACCCCTGGACCCTCTTGGTCGTCCTCCCACCTCTATAAATAGTTAGGTACCCCTTTAGAGTTTCTC[A/G]
GGTTCTGATAGATTAAAGTTTAGCCATTGCTACTTGCTTGTAGCGCACGTGTCAGCTAGACCGTCCGTCTGCTTGTTCTTCGAAACCCCAACTTATCATT

Reverse complement sequence

AATGATAAGTTGGGGTTTCGAAGAACAAGCAGACGGACGGTCTAGCTGACACGTGCGCTACAAGCAAGTAGCAATGGCTAAACTTTAATCTATCAGAACC[T/C]
GAGAAACTCTAAAGGGGTACCTAACTATTTATAGAGGTGGGAGGACGACCAAGAGGGTCCAGGGGTCATGCTACACCAGATTGGGTTGCACCCCACATGG

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 80.80% 16.60% 0.49% 2.07% NA
All Indica  2759 99.10% 0.40% 0.14% 0.33% NA
All Japonica  1512 43.50% 49.70% 1.06% 5.69% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.70% 0.00% 0.00% 0.33% NA
Indica Intermediate  786 98.50% 0.40% 0.38% 0.76% NA
Temperate Japonica  767 8.30% 83.70% 1.04% 6.91% NA
Tropical Japonica  504 87.90% 9.10% 0.20% 2.78% NA
Japonica Intermediate  241 62.70% 26.60% 2.90% 7.88% NA
VI/Aromatic  96 94.80% 3.10% 1.04% 1.04% NA
Intermediate  90 76.70% 20.00% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0319749387 A -> DEL N N silent_mutation Average:46.003; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg0319749387 A -> G LOC_Os03g35650.1 downstream_gene_variant ; 886.0bp to feature; MODIFIER silent_mutation Average:46.003; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N
vg0319749387 A -> G LOC_Os03g35650-LOC_Os03g35670 intergenic_region ; MODIFIER silent_mutation Average:46.003; most accessible tissue: Zhenshan97 flag leaf, score: 55.285 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319749387 NA 5.33E-06 mr1077 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
vg0319749387 6.15E-07 NA mr1210 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
vg0319749387 8.01E-06 NA mr1210 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
vg0319749387 7.53E-08 NA mr1586 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
vg0319749387 5.61E-06 NA mr1586 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
vg0319749387 NA 7.57E-13 mr1182_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
vg0319749387 7.01E-06 NA mr1305_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
vg0319749387 NA 5.23E-06 mr1379_2 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
vg0319749387 NA 3.71E-06 mr1559_2 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
vg0319749387 1.65E-06 NA mr1585_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
vg0319749387 NA 3.31E-11 mr1879_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
vg0319749387 NA 8.57E-07 mr1910_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
vg0319749387 6.92E-07 NA mr1933_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