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Detailed information for vg0620057664:

Variant ID: vg0620057664 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20057664
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTGGCTCGAGATTGAATCGCCTCCCTCAACAACAAAACTGTATATAATGTCTCCCTAAGAGAAGCATACATGTTGTAATCGTATGACGACTTAGCATA[G/A]
GTGGGTGAGAACAACTACTAGTGCTATCCAGCCGAGGGCCCGTGTACCCCTCTAAGGCTCTAATAATACACTATAATATGTTGGAATCAGGAAGGAGTGC

Reverse complement sequence

GCACTCCTTCCTGATTCCAACATATTATAGTGTATTATTAGAGCCTTAGAGGGGTACACGGGCCCTCGGCTGGATAGCACTAGTAGTTGTTCTCACCCAC[C/T]
TATGCTAAGTCGTCATACGATTACAACATGTATGCTTCTCTTAGGGAGACATTATATACAGTTTTGTTGTTGAGGGAGGCGATTCAATCTCGAGCCAGAC

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 65.00% 34.90% 0.08% 0.00% NA
All Indica  2759 95.10% 4.90% 0.04% 0.00% NA
All Japonica  1512 4.60% 95.30% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.10% 4.90% 0.00% 0.00% NA
Indica II  465 92.50% 7.50% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.30% 0.13% 0.00% NA
Temperate Japonica  767 3.10% 96.70% 0.13% 0.00% NA
Tropical Japonica  504 7.10% 92.70% 0.20% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 65.60% 34.40% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 1.11% 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
vg0620057664 G -> A LOC_Os06g34460.1 upstream_gene_variant ; 411.0bp to feature; MODIFIER silent_mutation Average:76.525; most accessible tissue: Callus, score: 85.652 N N N N
vg0620057664 G -> A LOC_Os06g34460-LOC_Os06g34470 intergenic_region ; MODIFIER silent_mutation Average:76.525; most accessible tissue: Callus, score: 85.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620057664 NA 6.42E-06 mr1216 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
vg0620057664 NA 1.32E-10 mr1325 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
vg0620057664 NA 7.53E-10 mr1336 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
vg0620057664 NA 5.13E-06 mr1532 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
vg0620057664 NA 8.42E-07 mr1690 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