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Detailed information for vg0310104151:

Variant ID: vg0310104151 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 10104151
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGGTCGACGAGCATCTCGTCCGGCGTGCACCATAGCCGGTCATGTCCTCCCCGTGTGCGTGGCTGCCGACGAGCTTTTTCTCCGTAGCCGGCCATCCT[C/T]
CCACAAGTCGGTCCCTCCCCTGTCTTGCTCGCGCGGCTGCCGATGAGCTTCTCCTCCGCAGCCAGCCATCCTCTCGCCCATTTGTCCCTCCCCTGCATCT

Reverse complement sequence

AGATGCAGGGGAGGGACAAATGGGCGAGAGGATGGCTGGCTGCGGAGGAGAAGCTCATCGGCAGCCGCGCGAGCAAGACAGGGGAGGGACCGACTTGTGG[G/A]
AGGATGGCCGGCTACGGAGAAAAAGCTCGTCGGCAGCCACGCACACGGGGAGGACATGACCGGCTATGGTGCACGCCGGACGAGATGCTCGTCGACCGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.40% 16.50% 0.13% 0.00% NA
All Indica  2759 73.50% 26.30% 0.22% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 67.90% 31.40% 0.67% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 60.60% 39.30% 0.11% 0.00% NA
Indica Intermediate  786 79.80% 20.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0310104151 C -> T LOC_Os03g18100.1 upstream_gene_variant ; 1448.0bp to feature; MODIFIER silent_mutation Average:66.474; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0310104151 C -> T LOC_Os03g18110.1 upstream_gene_variant ; 1830.0bp to feature; MODIFIER silent_mutation Average:66.474; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0310104151 C -> T LOC_Os03g18090.1 downstream_gene_variant ; 3211.0bp to feature; MODIFIER silent_mutation Average:66.474; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N
vg0310104151 C -> T LOC_Os03g18100-LOC_Os03g18110 intergenic_region ; MODIFIER silent_mutation Average:66.474; most accessible tissue: Minghui63 panicle, score: 83.421 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0310104151 2.47E-06 2.49E-06 mr1306 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
vg0310104151 NA 5.17E-07 mr1306 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
vg0310104151 NA 5.21E-07 mr1627 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
vg0310104151 NA 2.13E-07 mr1739 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
vg0310104151 NA 2.49E-06 mr1654_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