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Detailed information for vg1021478171:

Variant ID: vg1021478171 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 21478171
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACCAGCAGAAGGTTTACACGAAATAAATTAAGAGAAACGACACAAAGGCATCCTCTGATACCTGTCATCAAGATTTACATGAGAGAAAAAGAGAAAG[G/T]
AACAAAAGAAGAACCAAAGCAAAAGGAGAAAACAACAAGGAGGAAAAGAAGAGGCTGAGGCATGGAGTACAGAACAAAGCACCCATCCATTCCTCTCCTT

Reverse complement sequence

AAGGAGAGGAATGGATGGGTGCTTTGTTCTGTACTCCATGCCTCAGCCTCTTCTTTTCCTCCTTGTTGTTTTCTCCTTTTGCTTTGGTTCTTCTTTTGTT[C/A]
CTTTCTCTTTTTCTCTCATGTAAATCTTGATGACAGGTATCAGAGGATGCCTTTGTGTCGTTTCTCTTAATTTATTTCGTGTAAACCTTCTGCTGGTTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 3.90% 0.25% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 87.90% 11.30% 0.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 66.90% 31.20% 1.98% 0.00% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1021478171 G -> T LOC_Os10g40110.1 upstream_gene_variant ; 928.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021478171 G -> T LOC_Os10g40120.1 downstream_gene_variant ; 1254.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021478171 G -> T LOC_Os10g40130.1 downstream_gene_variant ; 4562.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021478171 G -> T LOC_Os10g40110-LOC_Os10g40120 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021478171 NA 1.44E-06 mr1471 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
vg1021478171 5.88E-07 1.76E-09 mr1925 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