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Detailed information for vg0330278992:

Variant ID: vg0330278992 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30278992
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:


CCAAACTTGTTCTTGTGTCAAAACTGCCCAAGATAGCTTGCCACCATGAGATGCAGGCATATACAGGCTTCAATGAATCATCCTACTGCTTTTCTTTTTT[C/T]
GGTTACTGTTTTCAGTGTTATTCTGTATAAGACATCAGTAAATGAGTGTAGGCCACCAAAGTATTGACAGAATTTGGATGCCGTGCACCTGTCTTAGTTC

Reverse complement sequence

GAACTAAGACAGGTGCACGGCATCCAAATTCTGTCAATACTTTGGTGGCCTACACTCATTTACTGATGTCTTATACAGAATAACACTGAAAACAGTAACC[G/A]
AAAAAAGAAAAGCAGTAGGATGATTCATTGAAGCCTGTATATGCCTGCATCTCATGGTGGCAAGCTATCTTGGGCAGTTTTGACACAAGAACAAGTTTGG

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 96.50% 2.20% 1.23% 0.00% NA
All Indica  2759 94.10% 3.80% 2.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 73.30% 17.60% 9.08% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 98.90% 0.00% 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
vg0330278992 C -> T LOC_Os03g52810.1 upstream_gene_variant ; 2991.0bp to feature; MODIFIER silent_mutation Average:51.728; most accessible tissue: Callus, score: 84.704 N N N N
vg0330278992 C -> T LOC_Os03g52794.1 intron_variant ; MODIFIER silent_mutation Average:51.728; most accessible tissue: Callus, score: 84.704 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330278992 NA 5.16E-06 mr1502 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
vg0330278992 NA 2.67E-08 mr1662 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
vg0330278992 NA 2.89E-06 mr1677 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
vg0330278992 NA 8.31E-07 mr1745 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
vg0330278992 NA 4.68E-06 mr1191_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
vg0330278992 NA 3.53E-07 mr1201_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