Search for Variation information by Variation ID:

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

Detailed information for vg0318866067:

Variant ID: vg0318866067 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18866067
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


CCACCGCTACTCCATCCACTCCAAAGGAGGAGCGATTCTGCATCATGGGAGTGCGAATTCCCAGCGGTAGGTATGGCAAAGGTTTACTCCGGCCTTTGAC[G/A]
GCATCGGAGAATGAGGGGGCAACAGAATCCCGTAGCCCTCCACCTATGAAGGTGAAGCATCACTTGACGCCCCCTCCAATCGTGAGGGCTCCCAGCAAAA

Reverse complement sequence

TTTTGCTGGGAGCCCTCACGATTGGAGGGGGCGTCAAGTGATGCTTCACCTTCATAGGTGGAGGGCTACGGGATTCTGTTGCCCCCTCATTCTCCGATGC[C/T]
GTCAAAGGCCGGAGTAAACCTTTGCCATACCTACCGCTGGGAATTCGCACTCCCATGATGCAGAATCGCTCCTCCTTTGGAGTGGATGGAGTAGCGGTGG

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 51.20% 32.50% 2.71% 13.58% NA
All Indica  2759 69.80% 3.00% 4.28% 22.94% NA
All Japonica  1512 12.80% 87.10% 0.00% 0.13% NA
Aus  269 89.60% 9.70% 0.74% 0.00% NA
Indica I  595 93.60% 2.50% 1.01% 2.86% NA
Indica II  465 41.50% 3.70% 2.58% 52.26% NA
Indica III  913 67.00% 1.10% 7.67% 24.21% NA
Indica Intermediate  786 71.80% 5.10% 3.82% 19.34% NA
Temperate Japonica  767 0.30% 99.60% 0.00% 0.13% NA
Tropical Japonica  504 34.10% 65.70% 0.00% 0.20% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 72.90% 3.12% 1.04% NA
Intermediate  90 41.10% 46.70% 5.56% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318866067 G -> A LOC_Os03g33000.1 synonymous_variant ; p.Thr112Thr; LOW synonymous_codon Average:29.977; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N
vg0318866067 G -> DEL LOC_Os03g33000.1 N frameshift_variant Average:29.977; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318866067 NA 3.38E-07 mr1136 Jap_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
vg0318866067 NA 1.48E-07 mr1217 Jap_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
vg0318866067 NA 5.77E-08 mr1439 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
vg0318866067 NA 8.70E-09 mr1607 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
vg0318866067 NA 1.79E-09 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
vg0318866067 NA 2.41E-06 mr1830 Jap_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
vg0318866067 NA 4.09E-07 mr1845 Jap_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
vg0318866067 NA 2.11E-24 mr1077_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
vg0318866067 NA 1.76E-08 mr1136_2 Jap_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
vg0318866067 NA 9.49E-13 mr1750_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
vg0318866067 1.29E-06 6.52E-08 mr1987_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