\

Search for Variation information by Variation ID:

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

Detailed information for vg0818043217:

Variant ID: vg0818043217 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18043217
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CGTTCCTACCAAGCTTCCTGAATGTAGCATAAGGCATCAAATTCACCGCGGCCCCACCATCGACCATCATCTTAGACATCGGCTTCCCATTGACGTAGCC[G/A]
TTTATATACAATGGTTTAAGATGCCGATTCTCTGTCCCCTCGGGTTTATCGAATACTGCCTGCTCTGGTGACGGAACCAACTTAGCCGATTCCTCTTCCA

Reverse complement sequence

TGGAAGAGGAATCGGCTAAGTTGGTTCCGTCACCAGAGCAGGCAGTATTCGATAAACCCGAGGGGACAGAGAATCGGCATCTTAAACCATTGTATATAAA[C/T]
GGCTACGTCAATGGGAAGCCGATGTCTAAGATGATGGTCGATGGTGGGGCCGCGGTGAATTTGATGCCTTATGCTACATTCAGGAAGCTTGGTAGGAACG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.20% 41.60% 2.56% 4.61% NA
All Indica  2759 28.00% 68.90% 2.32% 0.76% NA
All Japonica  1512 85.60% 1.60% 0.40% 12.43% NA
Aus  269 81.80% 1.50% 16.36% 0.37% NA
Indica I  595 37.80% 59.50% 2.69% 0.00% NA
Indica II  465 8.60% 90.10% 1.29% 0.00% NA
Indica III  913 27.30% 69.90% 0.99% 1.86% NA
Indica Intermediate  786 32.80% 62.50% 4.20% 0.51% NA
Temperate Japonica  767 98.70% 1.00% 0.00% 0.26% NA
Tropical Japonica  504 62.90% 2.00% 0.60% 34.52% NA
Japonica Intermediate  241 91.30% 2.50% 1.24% 4.98% NA
VI/Aromatic  96 91.70% 3.10% 1.04% 4.17% NA
Intermediate  90 52.20% 36.70% 6.67% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818043217 G -> A LOC_Os08g29430.1 synonymous_variant ; p.Asn737Asn; LOW synonymous_codon Average:43.166; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N
vg0818043217 G -> DEL LOC_Os08g29430.1 N frameshift_variant Average:43.166; most accessible tissue: Minghui63 flag leaf, score: 64.867 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818043217 NA 1.84E-06 mr1011 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
vg0818043217 NA 3.96E-09 mr1059 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
vg0818043217 7.51E-06 5.52E-10 mr1143 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
vg0818043217 NA 3.03E-09 mr1249 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
vg0818043217 NA 5.91E-10 mr1352 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
vg0818043217 NA 6.23E-10 mr1675 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
vg0818043217 NA 2.40E-07 mr1950 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
vg0818043217 2.84E-06 3.06E-10 mr1995 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
vg0818043217 8.96E-06 1.29E-09 mr1167_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
vg0818043217 NA 4.93E-06 mr1726_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
vg0818043217 NA 7.49E-06 mr1892_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
vg0818043217 NA 2.46E-07 mr1950_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