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Detailed information for vg0202715353:

Variant ID: vg0202715353 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2715353
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, G: 0.45, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


CTATGTGGTTTTCCATATCAATCACATATAAACTGGATTAGGGCTATTACCTTACGAGGGGTCTGAACCAGTATAATCTTTGTCTTCTTGTTTGCTTGAT[A/G]
TCGTATTGTGTATATCCTCGTACCAACATACCCCAATACTCCCATCCGGTCTACGGGTATCACATGTCGACACATTTTATGTCAGCTTGCGGCCATGCAC

Reverse complement sequence

GTGCATGGCCGCAAGCTGACATAAAATGTGTCGACATGTGATACCCGTAGACCGGATGGGAGTATTGGGGTATGTTGGTACGAGGATATACACAATACGA[T/C]
ATCAAGCAAACAAGAAGACAAAGATTATACTGGTTCAGACCCCTCGTAAGGTAATAGCCCTAATCCAGTTTATATGTGATTGATATGGAAAACCACATAG

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 33.90% 8.70% 0.80% 56.58% NA
All Indica  2759 7.20% 3.70% 1.09% 88.00% NA
All Japonica  1512 86.20% 13.00% 0.20% 0.60% NA
Aus  269 19.00% 2.20% 0.74% 78.07% NA
Indica I  595 12.10% 0.00% 1.18% 86.72% NA
Indica II  465 3.90% 1.50% 0.86% 93.76% NA
Indica III  913 7.00% 5.10% 0.88% 86.97% NA
Indica Intermediate  786 5.90% 6.00% 1.40% 86.77% NA
Temperate Japonica  767 80.20% 19.60% 0.13% 0.13% NA
Tropical Japonica  504 98.20% 0.40% 0.20% 1.19% NA
Japonica Intermediate  241 80.50% 18.30% 0.41% 0.83% NA
VI/Aromatic  96 0.00% 96.90% 0.00% 3.12% NA
Intermediate  90 53.30% 16.70% 3.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0202715353 A -> G LOC_Os02g05580.1 upstream_gene_variant ; 4031.0bp to feature; MODIFIER silent_mutation Average:11.842; most accessible tissue: Callus, score: 42.131 N N N N
vg0202715353 A -> G LOC_Os02g05590.1 downstream_gene_variant ; 2394.0bp to feature; MODIFIER silent_mutation Average:11.842; most accessible tissue: Callus, score: 42.131 N N N N
vg0202715353 A -> G LOC_Os02g05590-LOC_Os02g05600 intergenic_region ; MODIFIER silent_mutation Average:11.842; most accessible tissue: Callus, score: 42.131 N N N N
vg0202715353 A -> DEL N N silent_mutation Average:11.842; most accessible tissue: Callus, score: 42.131 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202715353 3.90E-09 NA mr1210 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
vg0202715353 2.81E-08 1.56E-11 mr1210 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
vg0202715353 8.84E-09 NA mr1305 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
vg0202715353 9.12E-08 2.25E-10 mr1305 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
vg0202715353 3.31E-10 3.31E-10 mr1409 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
vg0202715353 NA 9.81E-07 mr1515 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
vg0202715353 9.10E-08 6.21E-14 mr1585 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
vg0202715353 NA 1.79E-09 mr1585 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
vg0202715353 6.36E-08 NA mr1586 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
vg0202715353 2.84E-06 2.88E-09 mr1586 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
vg0202715353 8.45E-06 NA mr1765 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
vg0202715353 NA 2.27E-07 mr1765 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
vg0202715353 NA 1.67E-06 mr1788 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
vg0202715353 3.72E-07 NA mr1793 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
vg0202715353 5.76E-06 7.24E-07 mr1793 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
vg0202715353 NA 2.83E-07 mr1057_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
vg0202715353 3.03E-06 3.03E-06 mr1166_2 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
vg0202715353 7.32E-08 NA mr1305_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
vg0202715353 2.19E-08 4.88E-12 mr1305_2 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
vg0202715353 8.75E-06 2.74E-08 mr1409_2 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
vg0202715353 1.85E-06 2.96E-08 mr1559_2 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
vg0202715353 1.53E-08 3.52E-16 mr1585_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
vg0202715353 6.13E-07 4.76E-13 mr1585_2 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
vg0202715353 8.67E-06 8.67E-06 mr1649_2 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
vg0202715353 NA 1.02E-06 mr1765_2 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
vg0202715353 5.28E-06 NA mr1793_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
vg0202715353 6.95E-07 9.14E-09 mr1793_2 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