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Detailed information for vg0334582408:

Variant ID: vg0334582408 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34582408
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTATCTATAACCCTGACAGCACTCATAGAAAGCAAGACACCTATAGTGATTTTATCAATATAAGATATGCCTCGAGGGTGCTCATAGGACGCTCTGCAT[G/A]
CTCATTTTCCCTCCTCTCTCTAGATACCTAGTATTGATGGCTGCATGTTTCATACAAAGAATAAAGCTCCTTAGCAAGCTTTAATTTTTTTCCCTTAAAA

Reverse complement sequence

TTTTAAGGGAAAAAAATTAAAGCTTGCTAAGGAGCTTTATTCTTTGTATGAAACATGCAGCCATCAATACTAGGTATCTAGAGAGAGGAGGGAAAATGAG[C/T]
ATGCAGAGCGTCCTATGAGCACCCTCGAGGCATATCTTATATTGATAAAATCACTATAGGTGTCTTGCTTTCTATGAGTGCTGTCAGGGTTATAGATACC

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 94.90% 5.10% 0.04% 0.00% NA
All Indica  2759 91.70% 8.30% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 80.70% 19.10% 0.22% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0334582408 G -> A LOC_Os03g60850-LOC_Os03g60870 intergenic_region ; MODIFIER silent_mutation Average:43.814; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334582408 6.59E-06 3.63E-09 mr1970 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
vg0334582408 4.17E-06 1.39E-10 mr1973 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
vg0334582408 NA 1.98E-07 mr1798_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
vg0334582408 1.66E-06 2.21E-10 mr1970_2 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
vg0334582408 3.06E-06 1.27E-12 mr1973_2 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