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Detailed information for vg0620734924:

Variant ID: vg0620734924 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20734924
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTCACCAACATTCTATAATAAGCTACAGGGAACTGAAACAAGATACGACCAATTGTTTCCTTCTTTTGACATACTCCAAAACCATCCTAATTTCCAC[A/G]
ACTAAGTGAACTGCGCAAGGTAAACTATCTCTATCTACCATAAACAAAAAAAAGTTTTATCTTTAGAGATCTAGGGTCTGTATTTAGGGACCTTGTGTGA

Reverse complement sequence

TCACACAAGGTCCCTAAATACAGACCCTAGATCTCTAAAGATAAAACTTTTTTTTGTTTATGGTAGATAGAGATAGTTTACCTTGCGCAGTTCACTTAGT[T/C]
GTGGAAATTAGGATGGTTTTGGAGTATGTCAAAAGAAGGAAACAATTGGTCGTATCTTGTTTCAGTTCCCTGTAGCTTATTATAGAATGTTGGTGAGTTG

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 42.80% 15.40% 0.59% 41.18% NA
All Indica  2759 5.70% 24.90% 0.91% 68.47% NA
All Japonica  1512 97.40% 0.80% 0.07% 1.79% NA
Aus  269 92.20% 6.70% 0.00% 1.12% NA
Indica I  595 3.00% 4.20% 1.34% 91.43% NA
Indica II  465 6.70% 31.80% 1.08% 60.43% NA
Indica III  913 3.20% 39.90% 0.11% 56.85% NA
Indica Intermediate  786 10.20% 19.10% 1.40% 69.34% NA
Temperate Japonica  767 97.10% 1.30% 0.13% 1.43% NA
Tropical Japonica  504 97.20% 0.20% 0.00% 2.58% NA
Japonica Intermediate  241 98.30% 0.40% 0.00% 1.24% NA
VI/Aromatic  96 94.80% 0.00% 1.04% 4.17% NA
Intermediate  90 60.00% 13.30% 1.11% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620734924 A -> G LOC_Os06g35540.1 upstream_gene_variant ; 3153.0bp to feature; MODIFIER silent_mutation Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461 N N N N
vg0620734924 A -> G LOC_Os06g35550.1 downstream_gene_variant ; 1001.0bp to feature; MODIFIER silent_mutation Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461 N N N N
vg0620734924 A -> G LOC_Os06g35540-LOC_Os06g35550 intergenic_region ; MODIFIER silent_mutation Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461 N N N N
vg0620734924 A -> DEL N N silent_mutation Average:41.694; most accessible tissue: Minghui63 flower, score: 71.461 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620734924 NA 1.83E-06 mr1184_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
vg0620734924 NA 1.53E-06 mr1278_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
vg0620734924 NA 2.17E-07 mr1329_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
vg0620734924 NA 1.30E-06 mr1418_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
vg0620734924 3.23E-07 3.12E-07 mr1471_2 Ind_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
vg0620734924 NA 9.11E-07 mr1488_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
vg0620734924 NA 6.97E-08 mr1524_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
vg0620734924 1.75E-06 1.75E-06 mr1663_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
vg0620734924 NA 7.12E-08 mr1690_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
vg0620734924 NA 1.85E-06 mr1754_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
vg0620734924 NA 9.38E-06 mr1779_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
vg0620734924 1.03E-06 4.35E-07 mr1812_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
vg0620734924 3.08E-07 3.08E-07 mr1812_2 Ind_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
vg0620734924 2.91E-06 NA mr1832_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
vg0620734924 2.34E-06 2.34E-06 mr1832_2 Ind_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
vg0620734924 4.40E-06 NA mr1833_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
vg0620734924 1.33E-06 1.33E-06 mr1833_2 Ind_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
vg0620734924 2.18E-06 8.76E-06 mr1834_2 Ind_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
vg0620734924 3.01E-06 NA mr1843_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
vg0620734924 2.58E-06 2.58E-06 mr1843_2 Ind_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
vg0620734924 3.86E-06 3.86E-06 mr1847_2 Ind_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