\

Search for Variation information by Variation ID:

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

Detailed information for vg0323548805:

Variant ID: vg0323548805 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23548805
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGTCTGTGACCGGCCTGACACCGGTCACGTCTGACTGGACAGACAACCGTGCTCCCATGTCGCATCTGCCTCCGGCGGAGTGGAGGTAGGTATGACCC[G/A]
TTCCATCGGAGGGTCATTCGGAGGGCGGCCACCACAAGTCTTCACCCATTAATGAGGGAATGACAGGGCTGTCCCCCGTGTCAGGCGAGGGACGGCGCTG

Reverse complement sequence

CAGCGCCGTCCCTCGCCTGACACGGGGGACAGCCCTGTCATTCCCTCATTAATGGGTGAAGACTTGTGGTGGCCGCCCTCCGAATGACCCTCCGATGGAA[C/T]
GGGTCATACCTACCTCCACTCCGCCGGAGGCAGATGCGACATGGGAGCACGGTTGTCTGTCCAGTCAGACGTGACCGGTGTCAGGCCGGTCACAGACTGG

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 55.80% 39.80% 2.98% 1.42% NA
All Indica  2759 85.50% 8.20% 4.53% 1.74% NA
All Japonica  1512 0.50% 99.40% 0.07% 0.07% NA
Aus  269 85.10% 3.70% 5.58% 5.58% NA
Indica I  595 90.10% 1.80% 6.89% 1.18% NA
Indica II  465 84.30% 10.50% 4.73% 0.43% NA
Indica III  913 82.70% 11.20% 3.29% 2.85% NA
Indica Intermediate  786 86.10% 8.10% 4.07% 1.65% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 98.80% 0.20% 0.20% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 42.20% 54.40% 0.00% 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
vg0323548805 G -> A LOC_Os03g42320.1 upstream_gene_variant ; 1137.0bp to feature; MODIFIER silent_mutation Average:50.549; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 N N N N
vg0323548805 G -> A LOC_Os03g42320-LOC_Os03g42334 intergenic_region ; MODIFIER silent_mutation Average:50.549; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 N N N N
vg0323548805 G -> DEL N N silent_mutation Average:50.549; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323548805 NA 2.12E-28 mr1075 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
vg0323548805 NA 2.12E-39 mr1124 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
vg0323548805 NA 2.99E-19 mr1627 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
vg0323548805 NA 7.76E-14 mr1701 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
vg0323548805 NA 2.81E-115 mr1750 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
vg0323548805 NA 8.27E-06 mr1750 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
vg0323548805 NA 1.98E-54 mr1861 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
vg0323548805 NA 3.29E-15 mr1933 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
vg0323548805 NA 6.29E-55 mr1124_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
vg0323548805 4.37E-06 5.07E-06 mr1197_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
vg0323548805 NA 3.60E-19 mr1336_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
vg0323548805 NA 1.99E-23 mr1386_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
vg0323548805 NA 1.33E-14 mr1579_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