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Detailed information for vg0715958325:

Variant ID: vg0715958325 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15958325
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCAACGGCGTCAAAAATTTAGGGACAAAGGGAGTATCAATCAGGCTCCTTTGTCTCGCAGAGTTATAGCACCACATTGGGCTTGAATTTTCAGGAGCCC[C/G]
GGAAGTAATATGCACTCTAGCATCCTTGATTTTTTGCTACATACATGGGTGAGGACAACCTCAACAGGTTCCAAAATCAATTTCAGTAAGTCGTGCATGA

Reverse complement sequence

TCATGCACGACTTACTGAAATTGATTTTGGAACCTGTTGAGGTTGTCCTCACCCATGTATGTAGCAAAAAATCAAGGATGCTAGAGTGCATATTACTTCC[G/C]
GGGCTCCTGAAAATTCAAGCCCAATGTGGTGCTATAACTCTGCGAGACAAAGGAGCCTGATTGATACTCCCTTTGTCCCTAAATTTTTGACGCCGTTGAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.00% 34.90% 0.11% 0.00% NA
All Indica  2759 96.30% 3.60% 0.11% 0.00% NA
All Japonica  1512 7.50% 92.50% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.40% 0.38% 0.00% NA
Temperate Japonica  767 12.80% 87.20% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 51.10% 46.70% 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
vg0715958325 C -> G LOC_Os07g27400.1 downstream_gene_variant ; 2921.0bp to feature; MODIFIER silent_mutation Average:51.259; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0715958325 C -> G LOC_Os07g27390-LOC_Os07g27400 intergenic_region ; MODIFIER silent_mutation Average:51.259; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715958325 NA 1.98E-21 mr1155 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
vg0715958325 NA 4.74E-11 mr1630 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
vg0715958325 NA 4.83E-07 mr1915 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
vg0715958325 NA 1.42E-07 mr1004_2 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
vg0715958325 2.98E-06 2.98E-06 mr1004_2 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