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Detailed information for vg0601365150:

Variant ID: vg0601365150 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1365150
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AACTTCCATTACAATTCTGAAAACTCAAGGAATACAATAATACAACACCAATTTCTCATCTTTACATGGTCTGGGAAAAAAACAGTGTTTATCCTATTTA[C/A]
GTTGGCCCCTACATGCTCCTTAAGATTGTCCAAATTCTCCCCAGGACTGACATACAATAGGAGATCCTCAAGTATAGACTGGGCATCCGTCAACAACTAC

Reverse complement sequence

GTAGTTGTTGACGGATGCCCAGTCTATACTTGAGGATCTCCTATTGTATGTCAGTCCTGGGGAGAATTTGGACAATCTTAAGGAGCATGTAGGGGCCAAC[G/T]
TAAATAGGATAAACACTGTTTTTTTCCCAGACCATGTAAAGATGAGAAATTGGTGTTGTATTATTGTATTCCTTGAGTTTTCAGAATTGTAATGGAAGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.70% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 89.20% 10.80% 0.00% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 82.30% 17.70% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 19.50% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 21.90% 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
vg0601365150 C -> A LOC_Os06g03540.1 3_prime_UTR_variant ; 68.0bp to feature; MODIFIER silent_mutation Average:66.418; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg0601365150 C -> A LOC_Os06g03520.1 downstream_gene_variant ; 2641.0bp to feature; MODIFIER silent_mutation Average:66.418; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg0601365150 C -> A LOC_Os06g03530.1 intron_variant ; MODIFIER silent_mutation Average:66.418; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601365150 3.09E-06 NA mr1128_2 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
vg0601365150 7.07E-07 NA mr1252_2 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
vg0601365150 5.78E-06 7.73E-08 mr1252_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
vg0601365150 9.38E-06 NA mr1611_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
vg0601365150 NA 3.07E-07 mr1617_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