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Detailed information for vg0134962827:

Variant ID: vg0134962827 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34962827
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTGATCAATGGCGCATTTGAGCCCATTGTTGTCCATGGCCTTGGTGCTCGCTAGCTTCCTGCACACACACAAGAAAGAAACACCCACCATGCGACGTG[A/G]
GCAGAGGATTTCTGGTGGCTAATTGATGGAGTCTCGCTCATGGAGGAGTACTCACTTCCTCTCCTCGAGGAAGAAGTCCTTGAAGAGCTTGAGGCGGGTC

Reverse complement sequence

GACCCGCCTCAAGCTCTTCAAGGACTTCTTCCTCGAGGAGAGGAAGTGAGTACTCCTCCATGAGCGAGACTCCATCAATTAGCCACCAGAAATCCTCTGC[T/C]
CACGTCGCATGGTGGGTGTTTCTTTCTTGTGTGTGTGCAGGAAGCTAGCGAGCACCAAGGCCATGGACAACAATGGGCTCAAATGCGCCATTGATCACAT

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 55.60% 44.10% 0.06% 0.21% NA
All Indica  2759 26.10% 73.40% 0.07% 0.36% NA
All Japonica  1512 97.90% 2.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 10.30% 89.60% 0.17% 0.00% NA
Indica II  465 5.60% 94.00% 0.00% 0.43% NA
Indica III  913 37.60% 61.90% 0.00% 0.55% NA
Indica Intermediate  786 37.00% 62.50% 0.13% 0.38% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0134962827 A -> G LOC_Os01g60440.1 upstream_gene_variant ; 3472.0bp to feature; MODIFIER silent_mutation Average:73.307; most accessible tissue: Minghui63 flower, score: 85.573 N N N N
vg0134962827 A -> G LOC_Os01g60460.1 downstream_gene_variant ; 1316.0bp to feature; MODIFIER silent_mutation Average:73.307; most accessible tissue: Minghui63 flower, score: 85.573 N N N N
vg0134962827 A -> G LOC_Os01g60450.1 intron_variant ; MODIFIER silent_mutation Average:73.307; most accessible tissue: Minghui63 flower, score: 85.573 N N N N
vg0134962827 A -> DEL N N silent_mutation Average:73.307; most accessible tissue: Minghui63 flower, score: 85.573 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134962827 NA 8.26E-25 mr1003 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
vg0134962827 NA 3.57E-06 mr1003 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
vg0134962827 9.24E-06 1.11E-06 mr1008 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
vg0134962827 8.46E-06 NA mr1009 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
vg0134962827 2.15E-06 3.78E-06 mr1009 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
vg0134962827 NA 1.04E-23 mr1051 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
vg0134962827 NA 1.50E-09 mr1457 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
vg0134962827 NA 7.46E-07 mr1527 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
vg0134962827 NA 1.63E-19 mr1580 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
vg0134962827 NA 4.08E-07 mr1727 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
vg0134962827 NA 4.95E-06 mr1887 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
vg0134962827 6.80E-07 1.29E-07 mr1008_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
vg0134962827 NA 2.26E-08 mr1027_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
vg0134962827 NA 6.60E-27 mr1051_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
vg0134962827 NA 6.89E-06 mr1051_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
vg0134962827 NA 1.19E-18 mr1218_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
vg0134962827 NA 1.79E-26 mr1244_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
vg0134962827 NA 1.37E-11 mr1850_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