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Detailed information for vg1011171902:

Variant ID: vg1011171902 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11171902
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATAAAATAGGACTATACTGACAAGTGGAAGGTTCATCGTGTTTTTGACAAAATCACATTAAATGTTGTCCAGAAAATTCAGTCATATTTACAACGAC[A/G]
AAATCAATTTTACTTTGCAATTATAATTGTCCAAATCAACTATATCAACTCAAACCAAAATACATGATTAAATTAAGAAATGCGAAATTTGGAATGCACA

Reverse complement sequence

TGTGCATTCCAAATTTCGCATTTCTTAATTTAATCATGTATTTTGGTTTGAGTTGATATAGTTGATTTGGACAATTATAATTGCAAAGTAAAATTGATTT[T/C]
GTCGTTGTAAATATGACTGAATTTTCTGGACAACATTTAATGTGATTTTGTCAAAAACACGATGAACCTTCCACTTGTCAGTATAGTCCTATTTTATTTT

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 93.30% 2.50% 1.54% 2.71% NA
All Indica  2759 93.90% 4.10% 0.83% 1.09% NA
All Japonica  1512 99.40% 0.10% 0.07% 0.46% NA
Aus  269 70.30% 0.00% 12.64% 17.10% NA
Indica I  595 97.00% 1.30% 1.34% 0.34% NA
Indica II  465 84.90% 14.00% 0.65% 0.43% NA
Indica III  913 96.30% 1.50% 0.88% 1.31% NA
Indica Intermediate  786 94.30% 3.40% 0.51% 1.78% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 97.50% 0.00% 0.00% 2.49% NA
VI/Aromatic  96 41.70% 0.00% 13.54% 44.79% NA
Intermediate  90 94.40% 1.10% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1011171902 A -> G LOC_Os10g21760.1 upstream_gene_variant ; 4359.0bp to feature; MODIFIER silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1011171902 A -> G LOC_Os10g21780.1 upstream_gene_variant ; 1247.0bp to feature; MODIFIER silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1011171902 A -> G LOC_Os10g21784.1 upstream_gene_variant ; 4680.0bp to feature; MODIFIER silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1011171902 A -> G LOC_Os10g21770.1 downstream_gene_variant ; 181.0bp to feature; MODIFIER silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1011171902 A -> G LOC_Os10g21770-LOC_Os10g21780 intergenic_region ; MODIFIER silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N
vg1011171902 A -> DEL N N silent_mutation Average:41.848; most accessible tissue: Minghui63 flag leaf, score: 57.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011171902 NA 4.49E-07 mr1805_2 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
vg1011171902 3.77E-06 2.94E-06 mr1808_2 Ind_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