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Detailed information for vg0614725085:

Variant ID: vg0614725085 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14725085
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTGGTTCTATGCCAACCGTGCTGCTATCAACACCTGGGATAAATGCTCTACGGCATTCCTCTCGAAGTTCTTCCCGATGGGCAAAACCAACACCCTTT[G/A]
TGGACGAATTTCCAGCTTCCAGCAGACAAGGGACGAGTCCATTCCGGAAGCATGGGAACGACTGCAGGAGTACGTGGCCGCCTGTCCTCATCATGGGATG

Reverse complement sequence

CATCCCATGATGAGGACAGGCGGCCACGTACTCCTGCAGTCGTTCCCATGCTTCCGGAATGGACTCGTCCCTTGTCTGCTGGAAGCTGGAAATTCGTCCA[C/T]
AAAGGGTGTTGGTTTTGCCCATCGGGAAGAACTTCGAGAGGAATGCCGTAGAGCATTTATCCCAGGTGTTGATAGCAGCACGGTTGGCATAGAACCACTG

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 97.60% 1.60% 0.78% 0.00% NA
All Indica  2759 96.00% 2.70% 1.30% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 5.40% 1.85% 0.00% NA
Indica II  465 95.50% 3.20% 1.29% 0.00% NA
Indica III  913 99.30% 0.30% 0.33% 0.00% NA
Indica Intermediate  786 94.90% 3.10% 2.04% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0614725085 G -> A LOC_Os06g25170.1 missense_variant ; p.Cys125Tyr; MODERATE nonsynonymous_codon ; C125H Average:17.215; most accessible tissue: Zhenshan97 panicle, score: 28.447 benign -0.055 TOLERATED 0.17
vg0614725085 G -> A LOC_Os06g25170.1 missense_variant ; p.Cys125Tyr; MODERATE nonsynonymous_codon ; C125Y Average:17.215; most accessible tissue: Zhenshan97 panicle, score: 28.447 benign 1.242 TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614725085 4.28E-06 4.28E-06 mr1105 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