\

Search for Variation information by Variation ID:

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

Detailed information for vg0813705372:

Variant ID: vg0813705372 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13705372
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.05, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


ACATCTTCGCTTGGAAGCCGTCGGACATGCCTGGGGTCCCCAGGGAGGTGATCGAGCACCACCTCGCCGTGCGGTCGGATGCGTGACCCATCTGGCAGAA[G/C]
ATACGGCGCCAAGCCCCGGAGCGACAAGCCTTCATCCGCGAGGTGACGCGGCTCCTGGAGGCCGGCTTCATCCGAGAGGTCATCTACCCAGAGTGGCTGG

Reverse complement sequence

CCAGCCACTCTGGGTAGATGACCTCTCGGATGAAGCCGGCCTCCAGGAGCCGCGTCACCTCGCGGATGAAGGCTTGTCGCTCCGGGGCTTGGCGCCGTAT[C/G]
TTCTGCCAGATGGGTCACGCATCCGACCGCACGGCGAGGTGGTGCTCGATCACCTCCCTGGGGACCCCAGGCATGTCCGACGGCTTCCAAGCGAAGATGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.30% 48.20% 0.08% 0.40% NA
All Indica  2759 84.10% 15.40% 0.00% 0.54% NA
All Japonica  1512 1.90% 97.90% 0.20% 0.00% NA
Aus  269 16.40% 83.30% 0.00% 0.37% NA
Indica I  595 97.50% 2.00% 0.00% 0.50% NA
Indica II  465 87.50% 12.50% 0.00% 0.00% NA
Indica III  913 77.10% 21.90% 0.00% 0.99% NA
Indica Intermediate  786 79.90% 19.70% 0.00% 0.38% NA
Temperate Japonica  767 2.10% 97.80% 0.13% 0.00% NA
Tropical Japonica  504 1.20% 98.60% 0.20% 0.00% NA
Japonica Intermediate  241 2.90% 96.70% 0.41% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 33.30% 62.20% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0813705372 G -> C LOC_Os08g22790.1 missense_variant ; p.Asp398His; MODERATE nonsynonymous_codon ; D398R Average:71.722; most accessible tissue: Zhenshan97 young leaf, score: 86.852 unknown unknown TOLERATED 0.31
vg0813705372 G -> C LOC_Os08g22790.1 missense_variant ; p.Asp398His; MODERATE nonsynonymous_codon ; D398H Average:71.722; most accessible tissue: Zhenshan97 young leaf, score: 86.852 unknown unknown TOLERATED 1.00
vg0813705372 G -> DEL LOC_Os08g22790.1 N frameshift_variant Average:71.722; most accessible tissue: Zhenshan97 young leaf, score: 86.852 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813705372 NA 6.85E-07 mr1238 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
vg0813705372 NA 2.39E-13 mr1270 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
vg0813705372 NA 1.51E-06 mr1309 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
vg0813705372 NA 4.08E-09 mr1342 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
vg0813705372 NA 2.92E-28 mr1426 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
vg0813705372 NA 1.03E-15 mr1484 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
vg0813705372 NA 3.81E-11 mr1581 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
vg0813705372 NA 1.50E-12 mr1609 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
vg0813705372 4.40E-06 NA mr1704 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
vg0813705372 NA 2.06E-07 mr1716 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
vg0813705372 NA 1.59E-25 mr1841 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
vg0813705372 NA 6.04E-08 mr1841 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
vg0813705372 NA 1.03E-13 mr1883 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
vg0813705372 7.04E-06 7.04E-06 mr1883 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
vg0813705372 9.66E-07 9.65E-07 mr1900 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
vg0813705372 NA 5.78E-10 mr1945 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