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Detailed information for vg0405015610:

Variant ID: vg0405015610 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5015610
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.62, G: 0.39, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TCGCAACCAATTTTTCCACATCGACAAACAAGTTTGGTGTGAGTGGGATCATTGGTACTAAGCCCGAGAGCATGGCTTCCGTGGAACCACGGGGTGAAGC[A/G]
TCATCAACATCCTACATGAGTAATGCAATTATTGGGTAGATCTGTCGGTTCGTCACACGAACCGAGGCCAGTCAAGTTAACATGCACACTAGCAATGCAA

Reverse complement sequence

TTGCATTGCTAGTGTGCATGTTAACTTGACTGGCCTCGGTTCGTGTGACGAACCGACAGATCTACCCAATAATTGCATTACTCATGTAGGATGTTGATGA[T/C]
GCTTCACCCCGTGGTTCCACGGAAGCCATGCTCTCGGGCTTAGTACCAATGATCCCACTCACACCAAACTTGTTTGTCGATGTGGAAAAATTGGTTGCGA

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 31.10% 0.20% 6.31% 62.40% NA
All Indica  2759 11.00% 0.30% 9.53% 79.23% NA
All Japonica  1512 73.50% 0.10% 1.19% 25.20% NA
Aus  269 5.60% 0.00% 3.35% 91.08% NA
Indica I  595 8.60% 0.70% 5.38% 85.38% NA
Indica II  465 6.90% 0.00% 16.77% 76.34% NA
Indica III  913 12.20% 0.20% 8.98% 78.64% NA
Indica Intermediate  786 13.90% 0.10% 9.03% 76.97% NA
Temperate Japonica  767 92.80% 0.10% 0.00% 7.04% NA
Tropical Japonica  504 55.60% 0.20% 3.37% 40.87% NA
Japonica Intermediate  241 49.40% 0.00% 0.41% 50.21% NA
VI/Aromatic  96 11.50% 0.00% 4.17% 84.38% NA
Intermediate  90 33.30% 0.00% 4.44% 62.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405015610 A -> DEL N N silent_mutation Average:11.343; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N
vg0405015610 A -> G LOC_Os04g09390-LOC_Os04g09410 intergenic_region ; MODIFIER silent_mutation Average:11.343; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405015610 NA 2.42E-14 mr1035 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
vg0405015610 NA 8.77E-12 mr1626 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
vg0405015610 NA 2.26E-09 mr1637 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
vg0405015610 NA 2.03E-07 mr1804 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
vg0405015610 2.06E-07 7.00E-07 mr1826 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
vg0405015610 NA 2.64E-12 mr1844 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
vg0405015610 NA 1.27E-09 mr1945 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