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Detailed information for vg0513696601:

Variant ID: vg0513696601 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13696601
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCACCGAGAAGGCTAATCCCTGCATGCGAATCAAAGAACAGAAGCAAGAACAAGATAGATTGCAACACAATTGCATATGAATGATTAAGCACTCGAATTT[G/A]
GGGTTCCACAAACCGATCTAGCGGCGAAACTGTTCTTAACATATTGATCTAAGCAGAACCCGATTCTAAACGATGACGGCTACTGATTAAGTATGATTAG

Reverse complement sequence

CTAATCATACTTAATCAGTAGCCGTCATCGTTTAGAATCGGGTTCTGCTTAGATCAATATGTTAAGAACAGTTTCGCCGCTAGATCGGTTTGTGGAACCC[C/T]
AAATTCGAGTGCTTAATCATTCATATGCAATTGTGTTGCAATCTATCTTGTTCTTGCTTCTGTTCTTTGATTCGCATGCAGGGATTAGCCTTCTCGGTGA

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 75.40% 24.60% 0.04% 0.00% NA
All Indica  2759 86.60% 13.40% 0.04% 0.00% NA
All Japonica  1512 63.40% 36.50% 0.07% 0.00% NA
Aus  269 19.70% 80.30% 0.00% 0.00% NA
Indica I  595 87.10% 12.80% 0.17% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 76.00% 24.00% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.40% 0.00% 0.00% NA
Temperate Japonica  767 37.90% 61.90% 0.13% 0.00% NA
Tropical Japonica  504 92.70% 7.30% 0.00% 0.00% NA
Japonica Intermediate  241 83.40% 16.60% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0513696601 G -> A LOC_Os05g23830.1 intron_variant ; MODIFIER silent_mutation Average:43.219; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513696601 NA 9.47E-06 mr1030 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
vg0513696601 NA 6.51E-07 mr1157 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
vg0513696601 NA 6.97E-06 mr1164 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
vg0513696601 NA 7.78E-08 mr1229 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
vg0513696601 NA 5.17E-06 mr1330 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
vg0513696601 NA 6.00E-06 mr1530 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
vg0513696601 NA 2.56E-06 mr1548 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
vg0513696601 NA 2.74E-10 mr1596 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
vg0513696601 NA 2.74E-06 mr1596 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
vg0513696601 NA 3.46E-11 mr1627 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
vg0513696601 NA 2.94E-08 mr1763 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