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Detailed information for vg0715026108:

Variant ID: vg0715026108 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15026108
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGGCCGTGGGCCTCAGCTATATCTCTCCCTGCTAAATGGGAGAACAGCGCGCCTACTCACATCTCACTATGCAGATAATGCCACGATGTTCATCTGAC[C/T]
GACAAAGAGAGATATGAGACACCTCGCTCGAATTCGGCATTCCTTGGGGAAAGTTATGGGCCTCTAAACCAACATGGTGAAAAGTCAGATTCTGCGGCGC

Reverse complement sequence

GCGCCGCAGAATCTGACTTTTCACCATGTTGGTTTAGAGGCCCATAACTTTCCCCAAGGAATGCCGAATTCGAGCGAGGTGTCTCATATCTCTCTTTGTC[G/A]
GTCAGATGAACATCGTGGCATTATCTGCATAGTGAGATGTGAGTAGGCGCGCTGTTCTCCCATTTAGCAGGGAGAGATATAGCTGAGGCCCACGGCCTTC

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 94.10% 5.90% 0.02% 0.00% NA
All Indica  2759 95.00% 5.00% 0.00% 0.00% NA
All Japonica  1512 94.20% 5.70% 0.07% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 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 88.80% 11.20% 0.00% 0.00% NA
Temperate Japonica  767 89.30% 10.70% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 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
vg0715026108 C -> T LOC_Os07g26140.1 downstream_gene_variant ; 2775.0bp to feature; MODIFIER silent_mutation Average:54.519; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N
vg0715026108 C -> T LOC_Os07g26140-LOC_Os07g26150 intergenic_region ; MODIFIER silent_mutation Average:54.519; most accessible tissue: Zhenshan97 young leaf, score: 75.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715026108 NA 7.89E-06 mr1159_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
vg0715026108 3.11E-06 3.11E-06 mr1369_2 Ind_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
vg0715026108 1.86E-06 1.86E-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
vg0715026108 6.24E-06 3.53E-06 mr1832_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
vg0715026108 4.42E-06 1.95E-06 mr1833_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