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Detailed information for vg0220461014:

Variant ID: vg0220461014 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20461014
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGTCAAACAAGATGACAAAAGCACAGTGCAAAATAGCGGCGTCCGTATAGATGCATTCCAGGATCAAGTTGGGTCAAACACATACTACGGTCGCATTGA[A/G]
GAGATCTGGGAGCTAAACTACGCCAAGTTCAAGGTTCCTTTGTTCCACTGCCGTTGGGTGAATCTACGCACTGGTGTCAAAGCCGACAAGGAAGGTTTCA

Reverse complement sequence

TGAAACCTTCCTTGTCGGCTTTGACACCAGTGCGTAGATTCACCCAACGGCAGTGGAACAAAGGAACCTTGAACTTGGCGTAGTTTAGCTCCCAGATCTC[T/C]
TCAATGCGACCGTAGTATGTGTTTGACCCAACTTGATCCTGGAATGCATCTATACGGACGCCGCTATTTTGCACTGTGCTTTTGTCATCTTGTTTGACGG

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 38.70% 1.20% 36.46% 23.64% NA
All Indica  2759 6.20% 2.10% 57.16% 34.54% NA
All Japonica  1512 98.40% 0.00% 0.66% 0.93% NA
Aus  269 5.90% 0.00% 45.35% 48.70% NA
Indica I  595 3.50% 0.50% 50.08% 45.88% NA
Indica II  465 10.80% 0.90% 37.20% 51.18% NA
Indica III  913 5.00% 4.20% 76.23% 14.57% NA
Indica Intermediate  786 7.00% 1.50% 52.16% 39.31% NA
Temperate Japonica  767 99.00% 0.00% 0.26% 0.78% NA
Tropical Japonica  504 98.60% 0.00% 0.79% 0.60% NA
Japonica Intermediate  241 96.30% 0.00% 1.66% 2.07% NA
VI/Aromatic  96 95.80% 0.00% 2.08% 2.08% NA
Intermediate  90 67.80% 0.00% 13.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0220461014 A -> G LOC_Os02g34200.1 synonymous_variant ; p.Glu597Glu; LOW synonymous_codon Average:27.135; most accessible tissue: Minghui63 flag leaf, score: 55.781 N N N N
vg0220461014 A -> DEL LOC_Os02g34200.1 N frameshift_variant Average:27.135; most accessible tissue: Minghui63 flag leaf, score: 55.781 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220461014 NA 2.98E-06 mr1235 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
vg0220461014 NA 1.01E-08 mr1089_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
vg0220461014 NA 1.30E-10 mr1093_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
vg0220461014 NA 2.97E-09 mr1235_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
vg0220461014 NA 4.88E-07 mr1243_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
vg0220461014 NA 1.88E-06 mr1423_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
vg0220461014 1.11E-06 3.14E-07 mr1425_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
vg0220461014 NA 8.86E-06 mr1482_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
vg0220461014 NA 4.77E-10 mr1595_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
vg0220461014 NA 6.97E-10 mr1599_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
vg0220461014 NA 3.46E-08 mr1600_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
vg0220461014 NA 6.27E-14 mr1938_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