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Detailed information for vg1100096982:

Variant ID: vg1100096982 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 96982
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAACAAATTAAAACAAAACATACAGGGCCCATATGCTCCTTTAATTTTTCTTTTTAGATCAAACTGACACGTAAGCGTCACCTCAATGCCACGTGTGAT[A/G]
AAGACCTAGTTAAAAGAGACACATGGGCGCCATATCAGCTAAAACCAGGGACAATACTGTCAATGGACCTTATTTGCATTGGTTTTATAAGTTGGGGATG

Reverse complement sequence

CATCCCCAACTTATAAAACCAATGCAAATAAGGTCCATTGACAGTATTGTCCCTGGTTTTAGCTGATATGGCGCCCATGTGTCTCTTTTAACTAGGTCTT[T/C]
ATCACACGTGGCATTGAGGTGACGCTTACGTGTCAGTTTGATCTAAAAAGAAAAATTAAAGGAGCATATGGGCCCTGTATGTTTTGTTTTAATTTGTTAG

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 85.10% 10.50% 4.15% 0.30% NA
All Indica  2759 78.70% 14.60% 6.67% 0.00% NA
All Japonica  1512 98.00% 1.10% 0.07% 0.86% NA
Aus  269 78.80% 17.50% 3.72% 0.00% NA
Indica I  595 79.50% 14.80% 5.71% 0.00% NA
Indica II  465 90.50% 4.90% 4.52% 0.00% NA
Indica III  913 70.60% 21.40% 8.00% 0.00% NA
Indica Intermediate  786 80.40% 12.50% 7.12% 0.00% NA
Temperate Japonica  767 97.30% 1.00% 0.00% 1.69% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 77.80% 20.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100096982 A -> DEL N N silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01170.1 upstream_gene_variant ; 3842.0bp to feature; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01140.1 downstream_gene_variant ; 2869.0bp to feature; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01140.2 downstream_gene_variant ; 2869.0bp to feature; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01140.3 downstream_gene_variant ; 2869.0bp to feature; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01154.1 intron_variant ; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg1100096982 A -> G LOC_Os11g01154.4 intron_variant ; MODIFIER silent_mutation Average:17.094; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100096982 1.34E-06 NA mr1598 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
vg1100096982 NA 8.62E-07 mr1598 Ind_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