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Detailed information for vg0619254847:

Variant ID: vg0619254847 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19254847
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCATAGTGTGTCCTACTAGCGAGAGTCCACCCAACTTTCGCTCCTGAAGTCGCTGAGGGCATGGATTTCAAGCCCTCGGTTACAGACAAGGTCCACGG[C/T]
GCAGACCTGCTAGCTGGGTATACCAAGGTGTCCATCGATACAGTAAAGGACACCTGGTCAGGCTATCCGCTGCCCGTGCCCCCCAATGATGAAATCATGA

Reverse complement sequence

TCATGATTTCATCATTGGGGGGCACGGGCAGCGGATAGCCTGACCAGGTGTCCTTTACTGTATCGATGGACACCTTGGTATACCCAGCTAGCAGGTCTGC[G/A]
CCGTGGACCTTGTCTGTAACCGAGGGCTTGAAATCCATGCCCTCAGCGACTTCAGGAGCGAAAGTTGGGTGGACTCTCGCTAGTAGGACACACTATGCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 3.50% 1.21% 4.25% NA
All Indica  2759 93.30% 5.20% 1.49% 0.00% NA
All Japonica  1512 85.10% 0.70% 1.06% 13.16% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 91.20% 6.50% 2.37% 0.00% NA
Indica III  913 89.00% 9.10% 1.86% 0.00% NA
Indica Intermediate  786 94.70% 3.80% 1.53% 0.00% NA
Temperate Japonica  767 77.40% 1.20% 1.17% 20.21% NA
Tropical Japonica  504 97.40% 0.20% 0.60% 1.79% NA
Japonica Intermediate  241 83.40% 0.40% 1.66% 14.52% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 91.10% 7.80% 0.00% 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
vg0619254847 C -> T LOC_Os06g33070.1 synonymous_variant ; p.Gly447Gly; LOW synonymous_codon Average:44.678; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0619254847 C -> DEL LOC_Os06g33070.1 N frameshift_variant Average:44.678; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619254847 4.00E-06 NA mr1068 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
vg0619254847 2.23E-06 6.16E-09 mr1090 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
vg0619254847 5.14E-07 2.11E-09 mr1121 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
vg0619254847 4.63E-06 1.15E-09 mr1211 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
vg0619254847 6.76E-08 NA mr1068_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
vg0619254847 3.34E-08 2.56E-09 mr1090_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
vg0619254847 5.18E-06 NA mr1111_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
vg0619254847 4.23E-08 8.45E-10 mr1121_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
vg0619254847 3.19E-06 NA mr1200_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
vg0619254847 1.23E-08 3.13E-11 mr1211_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