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Detailed information for vg0317014991:

Variant ID: vg0317014991 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17014991
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACGGTCAGAACGACCTTTATCAGCCTTGTTCTTCATACGCAGCTGGGCTCGAGTTAACTGCTGCTGTAAAAATTCAGACAAGTGCTGCCTTTCAGTCT[A/G]
AACATCCACCACATCAGGCAGAGTAGCCAATGTCAGATCAGGAACTTGAGAATAATGAGGATCCACCCCAAAAAGAGCCTTATGAGGAGAACAGCCAAGA

Reverse complement sequence

TCTTGGCTGTTCTCCTCATAAGGCTCTTTTTGGGGTGGATCCTCATTATTCTCAAGTTCCTGATCTGACATTGGCTACTCTGCCTGATGTGGTGGATGTT[T/C]
AGACTGAAAGGCAGCACTTGTCTGAATTTTTACAGCAGCAGTTAACTCGAGCCCAGCTGCGTATGAAGAACAAGGCTGATAAAGGTCGTTCTGACCGTGT

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 96.00% 0.10% 3.83% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.60% 0.50% 11.90% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 81.00% 0.90% 18.12% 0.00% NA
Tropical Japonica  504 92.90% 0.00% 7.14% 0.00% NA
Japonica Intermediate  241 97.90% 0.00% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg0317014991 A -> G LOC_Os03g29850.1 upstream_gene_variant ; 3728.0bp to feature; MODIFIER silent_mutation Average:23.182; most accessible tissue: Minghui63 flower, score: 39.692 N N N N
vg0317014991 A -> G LOC_Os03g29864.1 intron_variant ; MODIFIER silent_mutation Average:23.182; most accessible tissue: Minghui63 flower, score: 39.692 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317014991 5.01E-06 NA mr1198 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
vg0317014991 NA 2.09E-07 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
vg0317014991 NA 2.67E-07 mr1585 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
vg0317014991 NA 4.10E-07 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
vg0317014991 1.21E-06 NA mr1897 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
vg0317014991 NA 4.39E-07 mr1897 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
vg0317014991 NA 2.05E-06 mr1305_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
vg0317014991 NA 1.66E-06 mr1585_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