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Detailed information for vg1020411439:

Variant ID: vg1020411439 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20411439
Reference Allele: AAlternative Allele: G,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAATCTAATTTGTTTCCCATTATTGACAATCCAAAAACCCATATTTAAGAAAGTACTTTTGACATTCATAAGACCAGACTAAAAATGAGAATCACCTT[A/G,C]
TTTCTTGTCAACTTGGGTTATAGATTTATTATAAATATATTTGAGTTTTTGCCGATGACAAAACTTTGATTTATTGTAACTGAAAGAACTAAGTATTCGA

Reverse complement sequence

TCGAATACTTAGTTCTTTCAGTTACAATAAATCAAAGTTTTGTCATCGGCAAAAACTCAAATATATTTATAATAAATCTATAACCCAAGTTGACAAGAAA[T/C,G]
AAGGTGATTCTCATTTTTAGTCTGGTCTTATGAATGTCAAAAGTACTTTCTTAAATATGGGTTTTTGGATTGTCAATAATGGGAAACAAATTAGATTTTG

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 86.50% 12.90% 0.51% 0.00% C: 0.02%
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 59.50% 38.90% 1.59% 0.00% C: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 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 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 35.70% 61.70% 2.61% 0.00% NA
Tropical Japonica  504 93.70% 6.30% 0.00% 0.00% NA
Japonica Intermediate  241 63.50% 34.40% 1.66% 0.00% C: 0.41%
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1020411439 A -> C LOC_Os10g38100.1 upstream_gene_variant ; 3438.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> C LOC_Os10g38110.1 downstream_gene_variant ; 505.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> C LOC_Os10g38110.2 downstream_gene_variant ; 505.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> C LOC_Os10g38100-LOC_Os10g38110 intergenic_region ; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> G LOC_Os10g38100.1 upstream_gene_variant ; 3438.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> G LOC_Os10g38110.1 downstream_gene_variant ; 505.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> G LOC_Os10g38110.2 downstream_gene_variant ; 505.0bp to feature; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N
vg1020411439 A -> G LOC_Os10g38100-LOC_Os10g38110 intergenic_region ; MODIFIER silent_mutation Average:25.513; most accessible tissue: Callus, score: 70.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020411439 NA 2.01E-06 mr1227_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
vg1020411439 NA 4.97E-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
vg1020411439 NA 2.19E-07 mr1446_2 Jap_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
vg1020411439 NA 8.19E-09 mr1940_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