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Detailed information for vg0806948099:

Variant ID: vg0806948099 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6948099
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCGGAACGTCGGAAACTAAAGCAATTAAACAAAAATCAACAAAACAGTACAAAAACAAGCATAAACAGTACATGTGGATAATTTTAACATGTAGATCTT[A/G]
ATTTTAGAAAAATTTAGCAACTTGAACTACCTGAAACGGATCTACGGTTATTTAGTTATGATTTTCCGAAGTTTTAATCTATTAGAAAATCGGAAAAAAG

Reverse complement sequence

CTTTTTTCCGATTTTCTAATAGATTAAAACTTCGGAAAATCATAACTAAATAACCGTAGATCCGTTTCAGGTAGTTCAAGTTGCTAAATTTTTCTAAAAT[T/C]
AAGATCTACATGTTAAAATTATCCACATGTACTGTTTATGCTTGTTTTTGTACTGTTTTGTTGATTTTTGTTTAATTGCTTTAGTTTCCGACGTTCCGGA

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 61.40% 1.60% 13.27% 23.66% NA
All Indica  2759 48.00% 0.10% 17.04% 34.90% NA
All Japonica  1512 87.70% 4.90% 1.46% 5.95% NA
Aus  269 54.60% 0.00% 42.01% 3.35% NA
Indica I  595 60.30% 0.20% 7.73% 31.76% NA
Indica II  465 49.00% 0.00% 14.84% 36.13% NA
Indica III  913 38.30% 0.00% 23.22% 38.44% NA
Indica Intermediate  786 49.10% 0.30% 18.19% 32.44% NA
Temperate Japonica  767 81.20% 9.60% 1.43% 7.69% NA
Tropical Japonica  504 95.60% 0.00% 1.98% 2.38% NA
Japonica Intermediate  241 91.70% 0.00% 0.41% 7.88% NA
VI/Aromatic  96 53.10% 0.00% 11.46% 35.42% NA
Intermediate  90 63.30% 0.00% 12.22% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0806948099 A -> G LOC_Os08g11850.1 downstream_gene_variant ; 1227.0bp to feature; MODIFIER silent_mutation Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0806948099 A -> G LOC_Os08g11840-LOC_Os08g11850 intergenic_region ; MODIFIER silent_mutation Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0806948099 A -> DEL N N silent_mutation Average:30.833; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806948099 NA 1.42E-07 mr1162 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
vg0806948099 2.01E-06 3.25E-06 mr1517 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
vg0806948099 2.68E-06 NA mr1844 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
vg0806948099 NA 2.53E-13 mr1900 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
vg0806948099 NA 1.96E-10 mr1905 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
vg0806948099 NA 2.08E-07 mr1915 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
vg0806948099 NA 5.82E-08 mr1004_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
vg0806948099 NA 2.82E-08 mr1205_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
vg0806948099 NA 3.90E-07 mr1302_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
vg0806948099 NA 5.84E-07 mr1824_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
vg0806948099 NA 1.23E-13 mr1838_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
vg0806948099 NA 3.00E-06 mr1928_2 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