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Detailed information for vg0402051312:

Variant ID: vg0402051312 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2051312
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTTTTCTATTCCTCTATTTTTTCAACCCTACGATTCAAAGGGGCCCTAAATGTCTTTTGGTGAATCCTTAGACCGTTTGATTGAACCACAGGAAAAAC[A/G]
CAGGAATTGGATGAGAGAGATAGACTCAAATAAAAGTTACCAAGAGGTTAAAGCTCTTGCTAAATTTCCTCCAAAATCTCTATAGGGTTGTCCATTCCAT

Reverse complement sequence

ATGGAATGGACAACCCTATAGAGATTTTGGAGGAAATTTAGCAAGAGCTTTAACCTCTTGGTAACTTTTATTTGAGTCTATCTCTCTCATCCAATTCCTG[T/C]
GTTTTTCCTGTGGTTCAATCAAACGGTCTAAGGATTCACCAAAAGACATTTAGGGCCCCTTTGAATCGTAGGGTTGAAAAAATAGAGGAATAGAAAAAAC

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 69.70% 29.80% 0.53% 0.00% NA
All Indica  2759 89.00% 10.90% 0.14% 0.00% NA
All Japonica  1512 48.50% 51.30% 0.20% 0.00% NA
Aus  269 13.80% 86.20% 0.00% 0.00% NA
Indica I  595 90.40% 9.40% 0.17% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 84.00% 15.80% 0.22% 0.00% NA
Indica Intermediate  786 88.50% 11.30% 0.13% 0.00% NA
Temperate Japonica  767 60.40% 39.50% 0.13% 0.00% NA
Tropical Japonica  504 44.40% 55.60% 0.00% 0.00% NA
Japonica Intermediate  241 19.50% 79.70% 0.83% 0.00% NA
VI/Aromatic  96 6.20% 75.00% 18.75% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0402051312 A -> G LOC_Os04g04360.1 upstream_gene_variant ; 3323.0bp to feature; MODIFIER silent_mutation Average:25.353; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg0402051312 A -> G LOC_Os04g04340-LOC_Os04g04360 intergenic_region ; MODIFIER silent_mutation Average:25.353; most accessible tissue: Minghui63 root, score: 40.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402051312 NA 8.49E-06 mr1164 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
vg0402051312 NA 8.20E-13 mr1465 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
vg0402051312 NA 3.67E-08 mr1707 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
vg0402051312 NA 7.73E-12 mr1720 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
vg0402051312 NA 2.52E-11 mr1794 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
vg0402051312 NA 1.00E-07 mr1794 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
vg0402051312 NA 2.20E-15 mr1180_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
vg0402051312 NA 6.22E-13 mr1189_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
vg0402051312 NA 7.42E-08 mr1834_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