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Detailed information for vg0226215115:

Variant ID: vg0226215115 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26215115
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGTTGCTAGTTGTTATTGTTATAGTGATCATGGGGGTCGATGTTGTGGAATCGTGCGGGAACTGTACAAAGGAGATCATGTTGTTGTCCTCAGCGCCA[C/T]
CGTTGCATTCAATCATGAAGCAAACGATGGCGCAGAGGGCCCGCGAGTTGCTTACGTAATGGCTATAGTCTGGGTTGAGACGCGTTGGAGAGCAAGGTGG

Reverse complement sequence

CCACCTTGCTCTCCAACGCGTCTCAACCCAGACTATAGCCATTACGTAAGCAACTCGCGGGCCCTCTGCGCCATCGTTTGCTTCATGATTGAATGCAACG[G/A]
TGGCGCTGAGGACAACAACATGATCTCCTTTGTACAGTTCCCGCACGATTCCACAACATCGACCCCCATGATCACTATAACAATAACAACTAGCAACACA

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 96.70% 2.80% 0.49% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 90.10% 8.50% 1.39% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 99.20% 0.10% 0.65% 0.00% NA
Tropical Japonica  504 73.40% 24.20% 2.38% 0.00% NA
Japonica Intermediate  241 95.90% 2.50% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 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
vg0226215115 C -> T LOC_Os02g43440.1 missense_variant ; p.Gly54Asp; MODERATE nonsynonymous_codon ; G54D Average:52.979; most accessible tissue: Zhenshan97 young leaf, score: 79.225 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226215115 2.26E-07 2.26E-07 mr1266 Jap_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
vg0226215115 NA 1.09E-06 mr1352 Jap_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
vg0226215115 4.82E-06 4.82E-06 mr1393 Jap_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
vg0226215115 6.89E-06 6.89E-06 mr1634 Jap_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
vg0226215115 NA 6.88E-06 mr1653 Jap_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
vg0226215115 2.43E-07 NA mr1754 Jap_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