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Detailed information for vg0707353401:

Variant ID: vg0707353401 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 7353401
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.34, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTACTAATCGTCATTGGAAATCTACACAAGAGTATAGCTCCCTCCCAAGGCCATGAAGTCCATGGGCGCTCTCATCATTGTGGTTCTTCTCCACTCC[T/C]
GAAGGTGAACCCCGAAACCTTCACCATCACGCCGAGTCTCCCACAATCATCTTGAGACATCACTGGCTAGGCACGCTAAGATGCCAAGAGTAACAGGAAG

Reverse complement sequence

CTTCCTGTTACTCTTGGCATCTTAGCGTGCCTAGCCAGTGATGTCTCAAGATGATTGTGGGAGACTCGGCGTGATGGTGAAGGTTTCGGGGTTCACCTTC[A/G]
GGAGTGGAGAAGAACCACAATGATGAGAGCGCCCATGGACTTCATGGCCTTGGGAGGGAGCTATACTCTTGTGTAGATTTCCAATGACGATTAGTAGAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 10.40% 0.08% 0.00% NA
All Indica  2759 94.90% 5.00% 0.07% 0.00% NA
All Japonica  1512 84.10% 15.90% 0.00% 0.00% NA
Aus  269 64.70% 35.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.30% 0.25% 0.00% NA
Temperate Japonica  767 96.70% 3.30% 0.00% 0.00% NA
Tropical Japonica  504 78.60% 21.40% 0.00% 0.00% NA
Japonica Intermediate  241 55.20% 44.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 2.22% 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
vg0707353401 T -> C LOC_Os07g12840.1 upstream_gene_variant ; 4808.0bp to feature; MODIFIER silent_mutation Average:56.363; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0707353401 T -> C LOC_Os07g12830.1 downstream_gene_variant ; 1719.0bp to feature; MODIFIER silent_mutation Average:56.363; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0707353401 T -> C LOC_Os07g12830.2 downstream_gene_variant ; 1719.0bp to feature; MODIFIER silent_mutation Average:56.363; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0707353401 T -> C LOC_Os07g12830.3 downstream_gene_variant ; 1719.0bp to feature; MODIFIER silent_mutation Average:56.363; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0707353401 T -> C LOC_Os07g12830-LOC_Os07g12840 intergenic_region ; MODIFIER silent_mutation Average:56.363; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707353401 2.21E-06 NA mr1064_2 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
vg0707353401 NA 2.67E-06 mr1064_2 Jap_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