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Detailed information for vg0602130119:

Variant ID: vg0602130119 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2130119
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGTGGATATATACCACAATGGAGTAAGTAGACAGGTTCAGTTTGCTGTCGTTACTTGTGGGTTGCTTTTTTGTGAATTTGCTCTGGAGAAAATGGCGG[A/G]
AAATTAAACATATTAATATGAGTCAATGGAAATGACTTGCAAGCAATTGCTAAACGAGAAATATCGGTTGCATGACGATATATATATATGGTCCCTTGAT

Reverse complement sequence

ATCAAGGGACCATATATATATATCGTCATGCAACCGATATTTCTCGTTTAGCAATTGCTTGCAAGTCATTTCCATTGACTCATATTAATATGTTTAATTT[T/C]
CCGCCATTTTCTCCAGAGCAAATTCACAAAAAAGCAACCCACAAGTAACGACAGCAAACTGAACCTGTCTACTTACTCCATTGTGGTATATATCCACCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.90% 10.30% 1.78% 0.00% NA
All Indica  2759 79.50% 17.50% 3.01% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 46.70% 43.20% 10.08% 0.00% NA
Indica II  465 73.10% 23.90% 3.01% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 85.20% 13.60% 1.15% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 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 92.20% 6.70% 1.11% 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
vg0602130119 A -> G LOC_Os06g04850-LOC_Os06g04860 intergenic_region ; MODIFIER silent_mutation Average:47.088; most accessible tissue: Zhenshan97 flower, score: 72.289 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602130119 NA 1.83E-07 mr1728 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
vg0602130119 NA 1.07E-09 mr1850 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
vg0602130119 1.00E-06 1.00E-06 mr1850 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
vg0602130119 NA 5.08E-11 mr1728_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