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Detailed information for vg0605538060:

Variant ID: vg0605538060 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5538060
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTTCCATCCGTAGATACCATATCTATCACGTGATAGATTTCCTTAACGTATACGAAAACTATTCGTACACGCGCGGGTATACCGCATCAGTATACAAC[A/G]
TGCATCTAAGGATAGAGAGTATATCTTATCCGTAACACTGACAAAATCTTATCAAACTTAAAAAGGTTTAAATAAAAAAAAGTCAAACAACTTACTCCCT

Reverse complement sequence

AGGGAGTAAGTTGTTTGACTTTTTTTTATTTAAACCTTTTTAAGTTTGATAAGATTTTGTCAGTGTTACGGATAAGATATACTCTCTATCCTTAGATGCA[T/C]
GTTGTATACTGATGCGGTATACCCGCGCGTGTACGAATAGTTTTCGTATACGTTAAGGAAATCTATCACGTGATAGATATGGTATCTACGGATGGAAGGA

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 85.80% 14.00% 0.17% 0.00% NA
All Indica  2759 94.60% 5.20% 0.18% 0.00% NA
All Japonica  1512 75.60% 24.20% 0.20% 0.00% NA
Aus  269 80.30% 19.70% 0.00% 0.00% NA
Indica I  595 98.70% 1.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 92.00% 8.00% 0.00% 0.00% NA
Indica Intermediate  786 91.70% 7.90% 0.38% 0.00% NA
Temperate Japonica  767 97.70% 2.10% 0.26% 0.00% NA
Tropical Japonica  504 42.30% 57.50% 0.20% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 18.80% 81.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0605538060 A -> G LOC_Os06g10620-LOC_Os06g10650 intergenic_region ; MODIFIER silent_mutation Average:57.169; most accessible tissue: Zhenshan97 panicle, score: 82.336 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605538060 NA 9.29E-12 mr1454 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
vg0605538060 NA 2.31E-07 mr1308_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
vg0605538060 3.57E-06 NA mr1480_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
vg0605538060 NA 8.55E-10 mr1578_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
vg0605538060 NA 6.39E-06 mr1735_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
vg0605538060 NA 8.63E-08 mr1819_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
vg0605538060 NA 5.90E-07 mr1819_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
vg0605538060 NA 9.80E-07 mr1860_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
vg0605538060 NA 9.24E-11 mr1952_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
vg0605538060 1.87E-06 NA mr1968_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