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Detailed information for vg0715010318:

Variant ID: vg0715010318 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15010318
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGACTAGGTATTTTGCCACATGGGTACGGACCCTTGAAATGCCTGCAGTAGAAATGATAGGACCAATTATAGAAAAGGCATGTGACATTATGACATTA[C/T]
AGAAAAATGGTCACCGTGTATTTTTGACCATTTTGTTGTATGAAAATGGTAGATGGGCACATGGGGGAAAAAATATTTGAGAAGTAATTTACACAGCATC

Reverse complement sequence

GATGCTGTGTAAATTACTTCTCAAATATTTTTTCCCCCATGTGCCCATCTACCATTTTCATACAACAAAATGGTCAAAAATACACGGTGACCATTTTTCT[G/A]
TAATGTCATAATGTCACATGCCTTTTCTATAATTGGTCCTATCATTTCTACTGCAGGCATTTCAAGGGTCCGTACCCATGTGGCAAAATACCTAGTCTGA

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 94.20% 5.80% 0.04% 0.00% NA
All Indica  2759 95.10% 4.90% 0.00% 0.00% NA
All Japonica  1512 94.40% 5.50% 0.07% 0.00% NA
Aus  269 93.70% 5.90% 0.37% 0.00% NA
Indica I  595 93.10% 6.90% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 89.20% 10.80% 0.00% 0.00% NA
Temperate Japonica  767 89.40% 10.40% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0715010318 C -> T LOC_Os07g26120.1 downstream_gene_variant ; 4852.0bp to feature; MODIFIER silent_mutation Average:64.136; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N
vg0715010318 C -> T LOC_Os07g26120-LOC_Os07g26130 intergenic_region ; MODIFIER silent_mutation Average:64.136; most accessible tissue: Minghui63 panicle, score: 77.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715010318 5.55E-06 5.55E-06 mr1369_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
vg0715010318 2.90E-06 2.90E-06 mr1453_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
vg0715010318 NA 9.33E-06 mr1706_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
vg0715010318 6.58E-06 3.12E-06 mr1832_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
vg0715010318 3.27E-06 1.22E-06 mr1833_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