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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0320153204:

Variant ID: vg0320153204 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20153204
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AACTCTTGTCGCACTCAGCTGTCCATTTAAACTTCTCATCTTTCTTAAGCAACTGAGTCATGGGTCGGGCGATCCTGGAGAAGTTTTCGATGAATCGGCG[A/G]
TAATAACCCGCAAGTCCAAGAAAACTCCAAATTTGCGACACAGTCTTAGGTGCGGTCCACTTGGTAACTGACTCCACATTCGATGGATCAACTGCCACGC

Reverse complement sequence

GCGTGGCAGTTGATCCATCGAATGTGGAGTCAGTTACCAAGTGGACCGCACCTAAGACTGTGTCGCAAATTTGGAGTTTTCTTGGACTTGCGGGTTATTA[T/C]
CGCCGATTCATCGAAAACTTCTCCAGGATCGCCCGACCCATGACTCAGTTGCTTAAGAAAGATGAGAAGTTTAAATGGACAGCTGAGTGCGACAAGAGTT

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 60.80% 32.60% 3.53% 3.05% NA
All Indica  2759 86.60% 3.60% 5.94% 3.91% NA
All Japonica  1512 12.00% 85.80% 0.00% 2.18% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 62.00% 5.70% 20.50% 11.76% NA
Indica II  465 93.80% 3.70% 2.15% 0.43% NA
Indica III  913 98.60% 1.30% 0.00% 0.11% NA
Indica Intermediate  786 87.00% 4.50% 4.07% 4.45% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 32.10% 65.50% 0.00% 2.38% NA
Japonica Intermediate  241 7.50% 83.80% 0.00% 8.71% NA
VI/Aromatic  96 25.00% 71.90% 1.04% 2.08% NA
Intermediate  90 46.70% 50.00% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0320153204 A -> DEL LOC_Os03g36330.1 N frameshift_variant Average:30.298; most accessible tissue: Minghui63 flag leaf, score: 62.47 N N N N
vg0320153204 A -> G LOC_Os03g36330.1 synonymous_variant ; p.Tyr64Tyr; LOW synonymous_codon Average:30.298; most accessible tissue: Minghui63 flag leaf, score: 62.47 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320153204 NA 9.56E-08 mr1136 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
vg0320153204 NA 8.23E-11 mr1188 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
vg0320153204 NA 2.97E-07 mr1227 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
vg0320153204 1.89E-07 3.50E-11 mr1334 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
vg0320153204 NA 6.66E-09 mr1575 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
vg0320153204 NA 2.31E-20 mr1588 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
vg0320153204 8.38E-08 1.51E-11 mr1718 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
vg0320153204 3.80E-07 NA mr1750 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
vg0320153204 1.14E-11 1.11E-21 mr1750 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
vg0320153204 NA 4.29E-06 mr1830 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
vg0320153204 3.85E-08 3.85E-08 mr1987 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
vg0320153204 NA 1.24E-08 mr1136_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
vg0320153204 NA 1.23E-24 mr1588_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
vg0320153204 1.69E-07 2.64E-13 mr1718_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
vg0320153204 NA 4.87E-11 mr1722_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
vg0320153204 NA 3.62E-18 mr1750_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
vg0320153204 NA 4.47E-06 mr1785_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
vg0320153204 NA 2.76E-15 mr1827_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