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Detailed information for vg0715867391:

Variant ID: vg0715867391 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15867391
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAACACTAACTTAATCAATAATCATGGGTTATGGATAGTCTAGCAAAATTAAAAGAGGGGACCAACGGGACTTGACTTATCGATTGGATTTTGATGCTG[C/T]
GGCCTGCAGTGGTGGAGTTGGTGGCGAACAGTGAACTGCTGGCCGATGTTGGGCATGGTAGGAGTAGGCGATACCGGCGGCCAGCGGCAGGCACGGCAAG

Reverse complement sequence

CTTGCCGTGCCTGCCGCTGGCCGCCGGTATCGCCTACTCCTACCATGCCCAACATCGGCCAGCAGTTCACTGTTCGCCACCAACTCCACCACTGCAGGCC[G/A]
CAGCATCAAAATCCAATCGATAAGTCAAGTCCCGTTGGTCCCCTCTTTTAATTTTGCTAGACTATCCATAACCCATGATTATTGATTAAGTTAGTGTTTG

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 97.30% 2.20% 0.19% 0.30% NA
All Indica  2759 99.70% 0.00% 0.00% 0.25% NA
All Japonica  1512 92.70% 6.70% 0.60% 0.00% NA
Aus  269 97.40% 0.00% 0.00% 2.60% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 99.40% 0.00% 0.00% 0.64% NA
Temperate Japonica  767 89.40% 9.80% 0.78% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 88.40% 10.80% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0715867391 C -> DEL N N silent_mutation Average:60.202; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N
vg0715867391 C -> T LOC_Os07g27290.1 downstream_gene_variant ; 4420.0bp to feature; MODIFIER silent_mutation Average:60.202; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N
vg0715867391 C -> T LOC_Os07g27300.1 downstream_gene_variant ; 1538.0bp to feature; MODIFIER silent_mutation Average:60.202; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N
vg0715867391 C -> T LOC_Os07g27300.2 downstream_gene_variant ; 2389.0bp to feature; MODIFIER silent_mutation Average:60.202; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N
vg0715867391 C -> T LOC_Os07g27290-LOC_Os07g27300 intergenic_region ; MODIFIER silent_mutation Average:60.202; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715867391 NA 3.20E-06 mr1100 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
vg0715867391 1.32E-06 1.32E-06 mr1237 Jap_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
vg0715867391 6.49E-06 6.49E-06 mr1581 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
vg0715867391 1.76E-06 4.16E-08 mr1613 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
vg0715867391 1.17E-07 1.17E-07 mr1795 Jap_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