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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0506835785:

Variant ID: vg0506835785 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6835785
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GCTCCCCACCGCCACCGCGCCATTGCCACCTCAGCGTCAAGTTTGCCGCCGGGTGCCGCCGCTCGACAAACGCACTCCGTCTCCTTGTCCTCCGTCGACC[G/A]
AACAACGGTCGTCGCCGCCTCATCGCGACCCTGTCCGTGCCGCCCCGGTGCCGTGATCATGACCCACGCCCCCGTGCGCCACCGACTCCCACTCACCACC

Reverse complement sequence

GGTGGTGAGTGGGAGTCGGTGGCGCACGGGGGCGTGGGTCATGATCACGGCACCGGGGCGGCACGGACAGGGTCGCGATGAGGCGGCGACGACCGTTGTT[C/T]
GGTCGACGGAGGACAAGGAGACGGAGTGCGTTTGTCGAGCGGCGGCACCCGGCGGCAAACTTGACGCTGAGGTGGCAATGGCGCGGTGGCGGTGGGGAGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.00% 41.70% 0.23% 0.02% NA
All Indica  2759 88.70% 11.00% 0.33% 0.00% NA
All Japonica  1512 4.80% 95.20% 0.00% 0.00% NA
Aus  269 70.60% 29.40% 0.00% 0.00% NA
Indica I  595 96.00% 4.00% 0.00% 0.00% NA
Indica II  465 80.00% 19.40% 0.65% 0.00% NA
Indica III  913 89.50% 10.30% 0.22% 0.00% NA
Indica Intermediate  786 87.30% 12.20% 0.51% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 35.60% 61.10% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0506835785 G -> DEL LOC_Os05g11960.1 N frameshift_variant Average:70.153; most accessible tissue: Callus, score: 81.775 N N N N
vg0506835785 G -> A LOC_Os05g11960.1 missense_variant ; p.Arg176Trp; MODERATE nonsynonymous_codon ; R176W Average:70.153; most accessible tissue: Callus, score: 81.775 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506835785 4.27E-10 1.32E-41 mr1039 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
vg0506835785 3.65E-07 3.14E-11 mr1039 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
vg0506835785 NA 4.65E-11 mr1514 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
vg0506835785 NA 9.98E-08 mr1593 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
vg0506835785 2.16E-07 1.93E-40 mr1632 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
vg0506835785 NA 1.59E-12 mr1632 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
vg0506835785 2.58E-08 6.78E-47 mr1873 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
vg0506835785 NA 1.33E-09 mr1873 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
vg0506835785 NA 4.78E-10 mr1904 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
vg0506835785 3.49E-06 4.38E-40 mr1039_2 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
vg0506835785 NA 8.52E-09 mr1039_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
vg0506835785 1.48E-08 4.12E-19 mr1514_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
vg0506835785 NA 1.82E-06 mr1514_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
vg0506835785 NA 5.18E-09 mr1593_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
vg0506835785 1.18E-11 1.32E-53 mr1632_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
vg0506835785 1.95E-07 5.24E-14 mr1632_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
vg0506835785 NA 7.12E-36 mr1873_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
vg0506835785 NA 3.10E-06 mr1873_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