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Detailed information for vg0415210679:

Variant ID: vg0415210679 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 15210679
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCTGCAAAAGATCCAAGCCTCTGTAGTGTCGGGGACCTCGCAGCCATTCACACTATATTTAAAAAGGGATTAGAATTTTAAAGATATAAGTAACAAGA[C/T]
AACCAGTGCATACCAGTTAAAATGACAAAATGAGACCACACATAGCTCTAGATCACACATCTCCATATCTCCAGTTACTAAATGGAAGTGTCTTATAGAA

Reverse complement sequence

TTCTATAAGACACTTCCATTTAGTAACTGGAGATATGGAGATGTGTGATCTAGAGCTATGTGTGGTCTCATTTTGTCATTTTAACTGGTATGCACTGGTT[G/A]
TCTTGTTACTTATATCTTTAAAATTCTAATCCCTTTTTAAATATAGTGTGAATGGCTGCGAGGTCCCCGACACTACAGAGGCTTGGATCTTTTGCAGAAT

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 68.30% 16.80% 4.72% 10.18% NA
All Indica  2759 65.20% 18.10% 6.81% 9.93% NA
All Japonica  1512 85.20% 0.50% 0.99% 13.29% NA
Aus  269 2.60% 97.00% 0.00% 0.37% NA
Indica I  595 65.70% 10.40% 1.18% 22.69% NA
Indica II  465 64.50% 30.50% 1.51% 3.44% NA
Indica III  913 58.50% 18.60% 15.33% 7.56% NA
Indica Intermediate  786 72.90% 15.90% 4.33% 6.87% NA
Temperate Japonica  767 77.70% 0.40% 1.04% 20.86% NA
Tropical Japonica  504 93.70% 0.20% 0.60% 5.56% NA
Japonica Intermediate  241 91.30% 1.70% 1.66% 5.39% NA
VI/Aromatic  96 71.90% 14.60% 12.50% 1.04% NA
Intermediate  90 72.20% 14.40% 8.89% 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
vg0415210679 C -> DEL N N silent_mutation Average:12.12; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 N N N N
vg0415210679 C -> T LOC_Os04g26120.1 intron_variant ; MODIFIER silent_mutation Average:12.12; most accessible tissue: Zhenshan97 flag leaf, score: 18.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0415210679 2.07E-06 1.26E-06 mr1094 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
vg0415210679 NA 1.16E-06 mr1130 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
vg0415210679 NA 6.24E-07 mr1193 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
vg0415210679 NA 4.10E-06 mr1589 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
vg0415210679 NA 3.62E-06 mr1637 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
vg0415210679 NA 9.80E-06 mr1669 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
vg0415210679 NA 2.52E-08 mr1951 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
vg0415210679 NA 5.34E-06 mr1968 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
vg0415210679 NA 6.88E-07 mr1188_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