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Detailed information for vg0722037631:

Variant ID: vg0722037631 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22037631
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTTCCCTCCTCCCCTAGATCAGCATTCCTTCTGCCTGATATGAGTTCGAAGAGCATCATGCCATAGCTGAAGACATCTGCCTTAGGAGTAATCGGCAC[A/G]
CCACTGATCCACTCAGGCGCAAGGTAACCCCTTGTCCCTCTCATTGTTGTCAAAACACGGCTGAAATCCCGCCCTAAGAGCTTTGCTAGACCAAAGTCAG

Reverse complement sequence

CTGACTTTGGTCTAGCAAAGCTCTTAGGGCGGGATTTCAGCCGTGTTTTGACAACAATGAGAGGGACAAGGGGTTACCTTGCGCCTGAGTGGATCAGTGG[T/C]
GTGCCGATTACTCCTAAGGCAGATGTCTTCAGCTATGGCATGATGCTCTTCGAACTCATATCAGGCAGAAGGAATGCTGATCTAGGGGAGGAGGGAAAGT

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 89.20% 10.80% 0.02% 0.00% NA
All Indica  2759 87.40% 12.60% 0.00% 0.00% NA
All Japonica  1512 94.30% 5.70% 0.00% 0.00% NA
Aus  269 74.00% 25.70% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 80.60% 19.40% 0.00% 0.00% NA
Indica III  913 80.90% 19.10% 0.00% 0.00% NA
Indica Intermediate  786 89.60% 10.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 86.30% 13.70% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 0.00% 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
vg0722037631 A -> G LOC_Os07g36780.1 synonymous_variant ; p.Gly668Gly; LOW synonymous_codon Average:70.317; most accessible tissue: Zhenshan97 flower, score: 76.539 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722037631 NA 7.21E-08 mr1188 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
vg0722037631 NA 5.59E-08 mr1188_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