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Detailed information for vg0611987652:

Variant ID: vg0611987652 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11987652
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTGCGCGCCGATGTTGTGGGAGGACGCAACACTGTCGGCGGCGAGCGCCACGGACGCGTACATGGCTAGGTGGAGGTACATGGTGGCGTGCTCGAGGG[C/T]
GTCCGTCTGGATAGTGAACGAGAGCAGTGGGAAGTCGACGAGCCGGTCCACGATGGCGAGCACGGAGAAGGAGAGGAGGAGGTAGCTGCCGTGCGGCCGC

Reverse complement sequence

GCGGCCGCACGGCAGCTACCTCCTCCTCTCCTTCTCCGTGCTCGCCATCGTGGACCGGCTCGTCGACTTCCCACTGCTCTCGTTCACTATCCAGACGGAC[G/A]
CCCTCGAGCACGCCACCATGTACCTCCACCTAGCCATGTACGCGTCCGTGGCGCTCGCCGCCGACAGTGTTGCGTCCTCCCACAACATCGGCGCGCAGGC

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 54.20% 45.70% 0.11% 0.00% NA
All Indica  2759 74.70% 25.20% 0.11% 0.00% NA
All Japonica  1512 9.30% 90.70% 0.00% 0.00% NA
Aus  269 92.20% 7.40% 0.37% 0.00% NA
Indica I  595 93.60% 6.10% 0.34% 0.00% NA
Indica II  465 86.50% 13.50% 0.00% 0.00% NA
Indica III  913 56.10% 43.80% 0.11% 0.00% NA
Indica Intermediate  786 75.20% 24.80% 0.00% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 20.40% 79.60% 0.00% 0.00% NA
Japonica Intermediate  241 9.50% 90.50% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 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
vg0611987652 C -> T LOC_Os06g20790.1 intron_variant ; MODIFIER silent_mutation Average:72.341; most accessible tissue: Zhenshan97 young leaf, score: 91.76 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611987652 NA 5.67E-06 mr1124 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
vg0611987652 NA 7.87E-07 mr1536 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
vg0611987652 NA 1.00E-07 mr1212_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
vg0611987652 NA 2.21E-12 mr1216_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
vg0611987652 NA 9.80E-16 mr1333_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
vg0611987652 NA 2.12E-09 mr1536_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
vg0611987652 NA 2.92E-15 mr1686_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
vg0611987652 NA 9.22E-07 mr1795_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