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Detailed information for vg0610070964:

Variant ID: vg0610070964 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10070964
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGAACGATTCAAGTAGATTGTATTCGGGGGTTTTACAATGAACCGGCCTTGTCCCTTAAATAGGGGTTGGTCTTGCCCTCTACAGGCCCTTCTCCATG[C/T]
CCAACTCGGGATAGAAACCAAAGGAAACACGGAACATGCCTTCCCGAGCAAGGAAACCCGAGACCCGACGTAAACAGACTCGGACTCGGACCCTGCCGGT

Reverse complement sequence

ACCGGCAGGGTCCGAGTCCGAGTCTGTTTACGTCGGGTCTCGGGTTTCCTTGCTCGGGAAGGCATGTTCCGTGTTTCCTTTGGTTTCTATCCCGAGTTGG[G/A]
CATGGAGAAGGGCCTGTAGAGGGCAAGACCAACCCCTATTTAAGGGACAAGGCCGGTTCATTGTAAAACCCCCGAATACAATCTACTTGAATCGTTCTTT

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 76.30% 23.70% 0.04% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 49.90% 50.10% 0.07% 0.00% NA
Aus  269 19.30% 80.70% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 64.30% 35.70% 0.00% 0.00% NA
Tropical Japonica  504 38.70% 61.10% 0.20% 0.00% NA
Japonica Intermediate  241 27.40% 72.60% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 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
vg0610070964 C -> T LOC_Os06g17370.1 upstream_gene_variant ; 1010.0bp to feature; MODIFIER silent_mutation Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596 N N N N
vg0610070964 C -> T LOC_Os06g17380.1 upstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596 N N N N
vg0610070964 C -> T LOC_Os06g17370-LOC_Os06g17380 intergenic_region ; MODIFIER silent_mutation Average:43.438; most accessible tissue: Zhenshan97 flower, score: 65.596 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610070964 NA 2.53E-07 mr1057 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
vg0610070964 NA 1.83E-08 mr1465 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
vg0610070964 6.35E-08 NA mr1679 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