\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0921842785:

Variant ID: vg0921842785 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21842785
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTACATTTTTTCTAAAATCAATTACTACATCCGTTGTTGTTCATAGGACGTAGGAGTACTTTGATGTCTAAAAGTCAAATTCTCTATAGATTTTGATC[A/G]
GTTGGTATAAAAATTCCTCTATGATGAGTCTACCAAGAAATTCATGTTTTAGACTAACAAGGTAATCCATTCATGTTTTAGACTAACAAGGTAATCCCTC

Reverse complement sequence

GAGGGATTACCTTGTTAGTCTAAAACATGAATGGATTACCTTGTTAGTCTAAAACATGAATTTCTTGGTAGACTCATCATAGAGGAATTTTTATACCAAC[T/C]
GATCAAAATCTATAGAGAATTTGACTTTTAGACATCAAAGTACTCCTACGTCCTATGAACAACAACGGATGTAGTAATTGATTTTAGAAAAAATGTACTA

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 91.30% 8.60% 0.06% 0.00% NA
All Indica  2759 91.20% 8.70% 0.07% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 48.00% 52.00% 0.00% 0.00% NA
Indica I  595 91.10% 8.70% 0.17% 0.00% NA
Indica II  465 81.70% 18.30% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 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
vg0921842785 A -> G LOC_Os09g37890.1 downstream_gene_variant ; 3797.0bp to feature; MODIFIER silent_mutation Average:58.67; most accessible tissue: Callus, score: 81.319 N N N N
vg0921842785 A -> G LOC_Os09g37880.1 intron_variant ; MODIFIER silent_mutation Average:58.67; most accessible tissue: Callus, score: 81.319 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921842785 NA 6.50E-07 mr1417 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
vg0921842785 NA 2.33E-06 mr1295_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
vg0921842785 1.44E-06 NA mr1622_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
vg0921842785 NA 2.74E-06 mr1729_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
vg0921842785 NA 4.49E-07 mr1740_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