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Detailed information for vg0618287415:

Variant ID: vg0618287415 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18287415
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCACAACACTCTAAACTCGCCGAGTTCCTCCGCATCTGTCCGCCTACCTTCTCTAGCTCCAATAACCCCGTGGATGCTTTGGATTGGTTGCATGTCGTGG[G/A]
GAAAAAGTTAGACACCGTGCAGTGCAATGATGAGGAGAAAGTCATCTTTGCCGCTCACCAACTGCAGGGGCCCGCATCTCTATGGTGGGACCACTTCCAG

Reverse complement sequence

CTGGAAGTGGTCCCACCATAGAGATGCGGGCCCCTGCAGTTGGTGAGCGGCAAAGATGACTTTCTCCTCATCATTGCACTGCACGGTGTCTAACTTTTTC[C/T]
CCACGACATGCAACCAATCCAAAGCATCCACGGGGTTATTGGAGCTAGAGAAGGTAGGCGGACAGATGCGGAGGAACTCGGCGAGTTTAGAGTGTTGTGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 0.20% 0.19% 1.63% NA
All Indica  2759 99.50% 0.30% 0.22% 0.00% NA
All Japonica  1512 94.80% 0.00% 0.13% 5.09% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 99.30% 0.30% 0.34% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 99.60% 0.20% 0.22% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 91.90% 0.00% 0.13% 7.95% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 93.40% 0.00% 0.41% 6.22% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0618287415 G -> A LOC_Os06g31420.1 missense_variant ; p.Gly375Glu; MODERATE nonsynonymous_codon ; G375E Average:10.242; most accessible tissue: Zhenshan97 flag leaf, score: 19.61 possibly damaging 1.967 TOLERATED 0.19
vg0618287415 G -> DEL LOC_Os06g31420.1 N frameshift_variant Average:10.242; most accessible tissue: Zhenshan97 flag leaf, score: 19.61 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618287415 2.96E-06 NA mr1707_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