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Detailed information for vg0714876939:

Variant ID: vg0714876939 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14876939
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTCCCCACTGTATATTATGAGGGGCATGCCGTCGGTCCTCACTAGCACTTGCCCAGCTTGAGACTCCGATGCTGTGGCGTGGAGCCTGGGTCCATCCG[G/A]
GTGCATCCCCAGTTGGCTCCCAACCTGCCTCATACATCTGCATGGGTGTTGAGGATGATGAACCTTCTTGTTCATTCCTTGCCATGTTGCGTGTCTCCCT

Reverse complement sequence

AGGGAGACACGCAACATGGCAAGGAATGAACAAGAAGGTTCATCATCCTCAACACCCATGCAGATGTATGAGGCAGGTTGGGAGCCAACTGGGGATGCAC[C/T]
CGGATGGACCCAGGCTCCACGCCACAGCATCGGAGTCTCAAGCTGGGCAAGTGCTAGTGAGGACCGACGGCATGCCCCTCATAATATACAGTGGGGAGAC

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 86.90% 7.90% 4.38% 0.78% NA
All Indica  2759 82.70% 10.20% 5.84% 1.27% NA
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 51.30% 31.60% 16.36% 0.74% NA
Indica I  595 80.20% 9.90% 6.89% 3.03% NA
Indica II  465 80.00% 13.30% 5.81% 0.86% NA
Indica III  913 85.80% 8.10% 5.26% 0.88% NA
Indica Intermediate  786 82.60% 11.10% 5.73% 0.64% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0714876939 G -> DEL LOC_Os07g25910.1 N frameshift_variant Average:31.851; most accessible tissue: Minghui63 young leaf, score: 47.146 N N N N
vg0714876939 G -> A LOC_Os07g25910.1 missense_variant ; p.Pro207Leu; MODERATE nonsynonymous_codon ; P207L Average:31.851; most accessible tissue: Minghui63 young leaf, score: 47.146 possibly damaging 1.777 TOLERATED 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714876939 NA 6.31E-07 mr1791 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
vg0714876939 6.56E-06 6.57E-06 mr1791 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