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Detailed information for vg0221768176:

Variant ID: vg0221768176 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21768176
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGATGAACGCTGCAGCACAGGAAAGAACTCGAGGCAAGTATAAGGAAGCAGCTCCAAGGAGTGGAATTATCACCATCCCCATATGACACTGCATGGGT[A/G]
GCTATGGTGCCACTCCGGGGTTCGTCTCACAATCCAAGCTTCCCTCAATGCGTCGACTGGATACTAGAGAATCAATGGGACGATGGATCATGGAGTATTG

Reverse complement sequence

CAATACTCCATGATCCATCGTCCCATTGATTCTCTAGTATCCAGTCGACGCATTGAGGGAAGCTTGGATTGTGAGACGAACCCCGGAGTGGCACCATAGC[T/C]
ACCCATGCAGTGTCATATGGGGATGGTGATAATTCCACTCCTTGGAGCTGCTTCCTTATACTTGCCTCGAGTTCTTTCCTGTGCTGCAGCGTTCATCACA

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 66.50% 33.20% 0.30% 0.00% NA
All Indica  2759 97.50% 2.20% 0.25% 0.00% NA
All Japonica  1512 8.50% 91.20% 0.33% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 98.30% 1.30% 0.34% 0.00% NA
Indica II  465 98.90% 0.90% 0.22% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.20% 0.51% 0.00% NA
Temperate Japonica  767 2.20% 97.30% 0.52% 0.00% NA
Tropical Japonica  504 19.40% 80.60% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.20% 0.41% 0.00% NA
VI/Aromatic  96 11.50% 87.50% 1.04% 0.00% NA
Intermediate  90 51.10% 47.80% 1.11% 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
vg0221768176 A -> G LOC_Os02g36140.2 synonymous_variant ; p.Val111Val; LOW synonymous_codon Average:69.017; most accessible tissue: Callus, score: 83.865 N N N N
vg0221768176 A -> G LOC_Os02g36140.5 synonymous_variant ; p.Val111Val; LOW synonymous_codon Average:69.017; most accessible tissue: Callus, score: 83.865 N N N N
vg0221768176 A -> G LOC_Os02g36140.4 synonymous_variant ; p.Val111Val; LOW synonymous_codon Average:69.017; most accessible tissue: Callus, score: 83.865 N N N N
vg0221768176 A -> G LOC_Os02g36140.3 synonymous_variant ; p.Val111Val; LOW synonymous_codon Average:69.017; most accessible tissue: Callus, score: 83.865 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221768176 NA 1.32E-40 mr1124 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
vg0221768176 NA 9.79E-29 mr1202 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
vg0221768176 NA 1.17E-08 mr1302 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
vg0221768176 NA 4.72E-12 mr1386 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
vg0221768176 NA 1.50E-06 mr1392 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
vg0221768176 NA 4.90E-14 mr1592 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
vg0221768176 NA 2.28E-06 mr1646 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
vg0221768176 NA 9.18E-14 mr1653 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
vg0221768176 NA 5.02E-11 mr1714 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
vg0221768176 7.70E-06 2.12E-07 mr1961 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
vg0221768176 NA 3.49E-38 mr1072_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
vg0221768176 NA 5.73E-38 mr1075_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
vg0221768176 NA 5.17E-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
vg0221768176 NA 2.41E-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
vg0221768176 NA 1.74E-06 mr1691_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