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Detailed information for vg1215215031:

Variant ID: vg1215215031 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15215031
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATTGTCTAAAAGAAAAATAATACAGGGCGAAAACCGGCCCAATTAATCTACACTACTACATATTACAGTACATAGTACTTCTTCCGTTTCACAATATA[A/T]
GTTATTCTAGCATTTCCCACGTTCATATGGATGTTCAATATGAATGTGGAAAATGCTAGAATGACTTATATTGTGAAACGGAGGGAGTATATATACACAT

Reverse complement sequence

ATGTGTATATATACTCCCTCCGTTTCACAATATAAGTCATTCTAGCATTTTCCACATTCATATTGAACATCCATATGAACGTGGGAAATGCTAGAATAAC[T/A]
TATATTGTGAAACGGAAGAAGTACTATGTACTGTAATATGTAGTAGTGTAGATTAATTGGGCCGGTTTTCGCCCTGTATTATTTTTCTTTTAGACAATGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 2.10% 1.33% 5.88% NA
All Indica  2759 89.80% 0.00% 0.33% 9.86% NA
All Japonica  1512 90.00% 6.40% 3.51% 0.07% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 98.80% 0.00% 0.17% 1.01% NA
Indica II  465 97.20% 0.00% 0.00% 2.80% NA
Indica III  913 81.30% 0.00% 0.66% 18.07% NA
Indica Intermediate  786 88.40% 0.10% 0.25% 11.20% NA
Temperate Japonica  767 85.50% 8.30% 6.13% 0.00% NA
Tropical Japonica  504 99.40% 0.20% 0.20% 0.20% NA
Japonica Intermediate  241 84.60% 13.30% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 0.00% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215215031 A -> DEL N N silent_mutation Average:41.667; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg1215215031 A -> T LOC_Os12g26120-LOC_Os12g26140 intergenic_region ; MODIFIER silent_mutation Average:41.667; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215215031 NA 3.48E-09 mr1100_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
vg1215215031 NA 7.18E-07 mr1203_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
vg1215215031 NA 1.45E-06 mr1613_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
vg1215215031 NA 4.90E-06 mr1619_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
vg1215215031 NA 2.33E-08 mr1913_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