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Detailed information for vg0709186195:

Variant ID: vg0709186195 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9186195
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGAGATGACAAAAATAAAAAAAGAAGTGCGTGTATATATGCACGTACATATACGAGATGTCAAAAATAAAAAAGAAGTGTGTGTATATGGTCCACCAC[G/A]
TCTGGTATTTTTCAATTTCTTTCTTTGTAGCCCTTAGGTTCTCCTTAAATTATACATATATGTAGCGACCACTCTTTGCGAGGTTGTCGAAGAAGCCACG

Reverse complement sequence

CGTGGCTTCTTCGACAACCTCGCAAAGAGTGGTCGCTACATATATGTATAATTTAAGGAGAACCTAAGGGCTACAAAGAAAGAAATTGAAAAATACCAGA[C/T]
GTGGTGGACCATATACACACACTTCTTTTTTATTTTTGACATCTCGTATATGTACGTGCATATATACACGCACTTCTTTTTTTATTTTTGTCATCTCTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 0.60% 0.49% 0.91% NA
All Indica  2759 98.30% 0.00% 0.14% 1.56% NA
All Japonica  1512 97.00% 1.80% 1.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 0.00% 0.34% 3.87% NA
Indica II  465 99.10% 0.00% 0.00% 0.86% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 0.00% 0.25% 2.04% NA
Temperate Japonica  767 94.00% 3.50% 2.48% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0709186195 G -> DEL N N silent_mutation Average:24.217; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N
vg0709186195 G -> A LOC_Os07g15820.1 downstream_gene_variant ; 2699.0bp to feature; MODIFIER silent_mutation Average:24.217; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N
vg0709186195 G -> A LOC_Os07g15800-LOC_Os07g15820 intergenic_region ; MODIFIER silent_mutation Average:24.217; most accessible tissue: Minghui63 young leaf, score: 42.042 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709186195 NA 6.86E-07 mr1028 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
vg0709186195 NA 3.83E-06 mr1453 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
vg0709186195 NA 2.34E-07 mr1652 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
vg0709186195 NA 8.66E-06 mr1697 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
vg0709186195 4.70E-06 4.70E-06 mr1074_2 Jap_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
vg0709186195 1.62E-06 1.62E-06 mr1081_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
vg0709186195 NA 7.47E-06 mr1298_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
vg0709186195 NA 9.12E-06 mr1318_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
vg0709186195 NA 2.96E-07 mr1510_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
vg0709186195 NA 2.80E-06 mr1702_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
vg0709186195 NA 8.95E-06 mr1731_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
vg0709186195 NA 2.10E-06 mr1788_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
vg0709186195 NA 9.50E-06 mr1986_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