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Detailed information for vg0603908292:

Variant ID: vg0603908292 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 3908292
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.04, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGCACTAGAATGCACGCATAAAAATTTTCTTGGTCACTCCATCAACGTTGACAACCCTATCAGGATGAGTATCGATGTGGTAGACCATACTGGAATTC[C/A]
TCTGCTTAATGGCTTGCAGCAAAGTGGGCAAACGGACATACGCTTCACCCCATTAACCGTAAATGAGCTTCATAGCCTCCTCTCGTGCCCTCCAAGCCTT

Reverse complement sequence

AAGGCTTGGAGGGCACGAGAGGAGGCTATGAAGCTCATTTACGGTTAATGGGGTGAAGCGTATGTCCGTTTGCCCACTTTGCTGCAAGCCATTAAGCAGA[G/T]
GAATTCCAGTATGGTCTACCACATCGATACTCATCCTGATAGGGTTGTCAACGTTGATGGAGTGACCAAGAAAATTTTTATGCGTGCATTCTAGTGCTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.80% 40.50% 12.59% 2.16% NA
All Indica  2759 17.00% 68.00% 12.14% 2.90% NA
All Japonica  1512 98.50% 0.60% 0.73% 0.13% NA
Aus  269 7.10% 1.90% 84.76% 6.32% NA
Indica I  595 15.00% 54.50% 23.19% 7.39% NA
Indica II  465 48.80% 45.20% 6.02% 0.00% NA
Indica III  913 2.60% 93.50% 3.72% 0.11% NA
Indica Intermediate  786 16.40% 62.00% 17.18% 4.45% NA
Temperate Japonica  767 99.00% 0.30% 0.65% 0.13% NA
Tropical Japonica  504 98.00% 1.40% 0.60% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 1.24% 0.41% NA
VI/Aromatic  96 90.60% 1.00% 7.29% 1.04% NA
Intermediate  90 57.80% 24.40% 15.56% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0603908292 C -> A LOC_Os06g08070.1 intron_variant ; MODIFIER silent_mutation Average:27.789; most accessible tissue: Minghui63 root, score: 38.567 N N N N
vg0603908292 C -> DEL N N silent_mutation Average:27.789; most accessible tissue: Minghui63 root, score: 38.567 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0603908292 NA 4.98E-06 mr1044 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
vg0603908292 NA 1.47E-11 mr1141 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
vg0603908292 NA 4.20E-07 mr1611 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
vg0603908292 NA 6.87E-08 mr1739 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
vg0603908292 NA 2.31E-07 mr1739 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
vg0603908292 NA 1.61E-07 mr1763 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
vg0603908292 NA 5.57E-08 mr1920 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
vg0603908292 NA 1.37E-06 mr1045_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
vg0603908292 NA 2.86E-12 mr1141_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
vg0603908292 NA 7.06E-06 mr1611_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
vg0603908292 NA 7.19E-06 mr1654_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
vg0603908292 NA 3.61E-06 mr1754_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