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Detailed information for vg0726584185:

Variant ID: vg0726584185 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26584185
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


AATAATGCAGAATCTGGTGATCAACCCCCGACTAGAATCCAGTCGGCCGAAGCCGAAGCCGGAGTTAATCAGGAGCCCCCGACTGGAAACCAGTCGGACG[C/T]
AGGGCCAAGCCAAGATATTCCAGAAGTCGAAACCCAAGCAGACAACCCTCGCGGACAAGACGCCAGCAATGACCGGAGATCTGGATCCCCTTTAAAAGCA

Reverse complement sequence

TGCTTTTAAAGGGGATCCAGATCTCCGGTCATTGCTGGCGTCTTGTCCGCGAGGGTTGTCTGCTTGGGTTTCGACTTCTGGAATATCTTGGCTTGGCCCT[G/A]
CGTCCGACTGGTTTCCAGTCGGGGGCTCCTGATTAACTCCGGCTTCGGCTTCGGCCGACTGGATTCTAGTCGGGGGTTGATCACCAGATTCTGCATTATT

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 42.90% 32.40% 16.59% 8.15% NA
All Indica  2759 12.90% 52.00% 24.79% 10.33% NA
All Japonica  1512 98.50% 1.20% 0.07% 0.26% NA
Aus  269 49.10% 19.70% 30.48% 0.74% NA
Indica I  595 15.00% 52.40% 24.37% 8.24% NA
Indica II  465 3.70% 72.90% 16.56% 6.88% NA
Indica III  913 12.70% 43.90% 29.46% 13.91% NA
Indica Intermediate  786 16.90% 48.70% 24.55% 9.80% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 1.40% 0.20% 0.40% NA
Japonica Intermediate  241 97.90% 1.20% 0.00% 0.83% NA
VI/Aromatic  96 5.20% 5.20% 7.29% 82.29% NA
Intermediate  90 52.20% 20.00% 11.11% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0726584185 C -> DEL LOC_Os07g44520.1 N frameshift_variant Average:26.594; most accessible tissue: Callus, score: 44.456 N N N N
vg0726584185 C -> T LOC_Os07g44520.1 missense_variant ; p.Ala369Val; MODERATE nonsynonymous_codon ; A369V Average:26.594; most accessible tissue: Callus, score: 44.456 benign 0.563 TOLERATED 0.63

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726584185 1.13E-06 8.93E-07 mr1940 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
vg0726584185 NA 7.10E-08 mr1690_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