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Detailed information for vg0335583124:

Variant ID: vg0335583124 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35583124
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAAGAACTAACGGTGCAGTAGCTGATGGCAGTGATAAATCGTAACCATAACAAACTTAGGGCGTGTTTGGATAGTGCCCTGACCTGATCGCTCTCATT[C/T]
AGACGGGTGCATCCAACCACAGACCACCAAAATCGGACGCCTGAGAATCGTGCCTGACTTAGGCGTGATTCTCAGGGTGTGAAGCAAACAAACCCTTAAT

Reverse complement sequence

ATTAAGGGTTTGTTTGCTTCACACCCTGAGAATCACGCCTAAGTCAGGCACGATTCTCAGGCGTCCGATTTTGGTGGTCTGTGGTTGGATGCACCCGTCT[G/A]
AATGAGAGCGATCAGGTCAGGGCACTATCCAAACACGCCCTAAGTTTGTTATGGTTACGATTTATCACTGCCATCAGCTACTGCACCGTTAGTTCTTTTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.00% 11.40% 0.59% 0.00% NA
All Indica  2759 84.30% 14.80% 0.94% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 61.30% 38.70% 0.00% 0.00% NA
Indica I  595 88.10% 10.10% 1.85% 0.00% NA
Indica II  465 49.50% 48.20% 2.37% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 14.80% 0.51% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 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 77.80% 20.00% 2.22% 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
vg0335583124 C -> T LOC_Os03g62900.1 downstream_gene_variant ; 378.0bp to feature; MODIFIER silent_mutation Average:68.822; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N
vg0335583124 C -> T LOC_Os03g62880-LOC_Os03g62900 intergenic_region ; MODIFIER silent_mutation Average:68.822; most accessible tissue: Zhenshan97 panicle, score: 87.126 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335583124 NA 2.44E-13 mr1141 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
vg0335583124 NA 7.62E-09 mr1536 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
vg0335583124 NA 9.90E-06 mr1918 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
vg0335583124 NA 3.36E-11 mr1141_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
vg0335583124 NA 2.55E-08 mr1536_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
vg0335583124 NA 2.91E-06 mr1732_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