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Detailed information for vg0333155926:

Variant ID: vg0333155926 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 33155926
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAGTTCACCACCTTCGGAGTGAAGGAAGAACTACCCCGAGTGATTGAGGCTTGGGTAGTCCTCTCCGTGGGCCGGCTCCCGCCTTGCCCACCCCTTGA[C/T]
GAAGGGAGCGTGTGGTGGCTTCGTGGTTGAGCGGTGGAGTTGGGCTCGCCTCAACGGGGATTAGGAAACCGGCGAGTTTCTGAACCTCGGTGAAAAATTC

Reverse complement sequence

GAATTTTTCACCGAGGTTCAGAAACTCGCCGGTTTCCTAATCCCCGTTGAGGCGAGCCCAACTCCACCGCTCAACCACGAAGCCACCACACGCTCCCTTC[G/A]
TCAAGGGGTGGGCAAGGCGGGAGCCGGCCCACGGAGAGGACTACCCAAGCCTCAATCACTCGGGGTAGTTCTTCCTTCACTCCGAAGGTGGTGAACTCCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.00% 40.90% 6.35% 0.78% NA
All Indica  2759 78.30% 9.80% 10.62% 1.34% NA
All Japonica  1512 0.70% 99.20% 0.13% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 72.60% 10.30% 16.81% 0.34% NA
Indica II  465 75.70% 8.20% 15.91% 0.22% NA
Indica III  913 85.90% 5.30% 5.70% 3.18% NA
Indica Intermediate  786 75.20% 15.60% 8.52% 0.64% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.60% 0.20% 0.00% NA
Japonica Intermediate  241 0.00% 99.60% 0.41% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 35.60% 58.90% 5.56% 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
vg0333155926 C -> T LOC_Os03g58220.1 intron_variant ; MODIFIER silent_mutation Average:30.617; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N
vg0333155926 C -> DEL N N silent_mutation Average:30.617; most accessible tissue: Minghui63 panicle, score: 59.629 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333155926 NA 3.27E-34 mr1723 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
vg0333155926 4.42E-08 5.45E-42 mr1723_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
vg0333155926 1.95E-06 1.35E-08 mr1723_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