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Detailed information for vg0708904930:

Variant ID: vg0708904930 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8904930
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TGAATCTAGAATAGTATAATATATCAATCGTATGTCCCCGATAAATTCTATGTAATAAGTTCTATATACAAACCAGTGTCAACAATCGTCAAGTTATATT[G/A]
TTTATGATACATCCATGCACAATGCAATTAATAATTAGTTGACATCCAATATGCACGTGCGTCATCAAGCACCGAAGATATATGATGATACTTAGTGGGA

Reverse complement sequence

TCCCACTAAGTATCATCATATATCTTCGGTGCTTGATGACGCACGTGCATATTGGATGTCAACTAATTATTAATTGCATTGTGCATGGATGTATCATAAA[C/T]
AATATAACTTGACGATTGTTGACACTGGTTTGTATATAGAACTTATTACATAGAATTTATCGGGGACATACGATTGATATATTATACTATTCTAGATTCA

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 85.10% 14.70% 0.21% 0.00% NA
All Indica  2759 74.70% 24.90% 0.36% 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 22.40% 76.50% 1.18% 0.00% NA
Indica II  465 91.60% 8.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 75.60% 24.00% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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% 7.80% 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
vg0708904930 G -> A LOC_Os07g15410.1 downstream_gene_variant ; 626.0bp to feature; MODIFIER silent_mutation Average:32.183; most accessible tissue: Minghui63 young leaf, score: 47.146 N N N N
vg0708904930 G -> A LOC_Os07g15400-LOC_Os07g15410 intergenic_region ; MODIFIER silent_mutation Average:32.183; most accessible tissue: Minghui63 young leaf, score: 47.146 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0708904930 NA 3.26E-08 mr1565 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
vg0708904930 2.71E-06 NA mr1686 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
vg0708904930 NA 4.93E-06 mr1629_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