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Detailed information for vg0333199277:

Variant ID: vg0333199277 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 33199277
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAGTTTAACGTAATATGCAACAAATCTCCCCCTAAACCTTGTGCTCGCGACTTACTTCCAAAACCCCGATCCGCGAGCGTAGCTCCTCAAACCGCACT[C/T]
GACCAAGGGACTTCGTCAGTATATCAGTGACTTGATATGCAGTCCCAGTGAATTCCAACTGAACTCGACCTTCTTCCACACACTCCCGGATATAATGATA

Reverse complement sequence

TATCATTATATCCGGGAGTGTGTGGAAGAAGGTCGAGTTCAGTTGGAATTCACTGGGACTGCATATCAAGTCACTGATATACTGACGAAGTCCCTTGGTC[G/A]
AGTGCGGTTTGAGGAGCTACGCTCGCGGATCGGGGTTTTGGAAGTAAGTCGCGAGCACAAGGTTTAGGGGGAGATTTGTTGCATATTACGTTAAACTTGT

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 51.00% 48.90% 0.13% 0.00% NA
All Indica  2759 26.40% 73.40% 0.22% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 5.90% 94.10% 0.00% 0.00% NA
Indica I  595 14.50% 85.40% 0.17% 0.00% NA
Indica II  465 57.40% 41.90% 0.65% 0.00% NA
Indica III  913 13.60% 86.30% 0.11% 0.00% NA
Indica Intermediate  786 31.80% 68.10% 0.13% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0333199277 C -> T LOC_Os03g58270.1 missense_variant ; p.Arg1169Gln; MODERATE nonsynonymous_codon ; R1169Q Average:57.191; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 possibly damaging 1.569 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333199277 NA 8.17E-13 mr1069 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
vg0333199277 NA 7.45E-15 mr1441 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
vg0333199277 NA 3.59E-06 mr1441 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
vg0333199277 1.48E-08 2.37E-37 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
vg0333199277 8.00E-08 6.13E-10 mr1723 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
vg0333199277 NA 5.88E-07 mr1062_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
vg0333199277 NA 3.02E-26 mr1441_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
vg0333199277 6.14E-12 1.67E-43 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
vg0333199277 2.55E-10 2.07E-13 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