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Detailed information for vg0318103123:

Variant ID: vg0318103123 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18103123
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TACCACTTGCCAGATCTCAACTGGCTCCCCTTCTATTTGGTGGGGTACTTTTCGTGACTTTGAGTATGATAGTCCCTCTTGCCCTATTTTCACCAGATGT[C/G]
TCCGGTTACTTTAGGGTCATGAGGAGCTGAAGTTTCTTGTCCAATTGTTTTTATTCGAGGCCTCTAGACAAGATGAGGGATACATTTACTTTCTTCGGTA

Reverse complement sequence

TACCGAAGAAAGTAAATGTATCCCTCATCTTGTCTAGAGGCCTCGAATAAAAACAATTGGACAAGAAACTTCAGCTCCTCATGACCCTAAAGTAACCGGA[G/C]
ACATCTGGTGAAAATAGGGCAAGAGGGACTATCATACTCAAAGTCACGAAAAGTACCCCACCAAATAGAAGGGGAGCCAGTTGAGATCTGGCAAGTGGTA

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 56.50% 43.40% 0.08% 0.00% NA
All Indica  2759 28.10% 71.80% 0.11% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 91.80% 8.20% 0.00% 0.00% NA
Indica I  595 44.00% 55.80% 0.17% 0.00% NA
Indica II  465 14.60% 85.40% 0.00% 0.00% NA
Indica III  913 29.40% 70.60% 0.00% 0.00% NA
Indica Intermediate  786 22.60% 77.10% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318103123 C -> G LOC_Os03g31700.1 downstream_gene_variant ; 2073.0bp to feature; MODIFIER silent_mutation Average:43.228; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N
vg0318103123 C -> G LOC_Os03g31700-LOC_Os03g31706 intergenic_region ; MODIFIER silent_mutation Average:43.228; most accessible tissue: Minghui63 flag leaf, score: 60.569 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318103123 NA 2.80E-06 mr1221 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
vg0318103123 NA 2.49E-06 mr1532 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
vg0318103123 NA 1.35E-08 mr1045_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
vg0318103123 NA 4.25E-06 mr1220_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
vg0318103123 NA 1.22E-09 mr1221_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
vg0318103123 NA 3.84E-07 mr1358_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
vg0318103123 6.00E-07 3.79E-08 mr1391_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
vg0318103123 NA 1.00E-07 mr1498_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
vg0318103123 NA 4.81E-09 mr1624_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
vg0318103123 NA 6.04E-06 mr1785_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
vg0318103123 NA 8.17E-08 mr1804_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
vg0318103123 NA 7.53E-08 mr1837_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
vg0318103123 NA 1.55E-10 mr1850_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
vg0318103123 NA 1.85E-08 mr1925_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
vg0318103123 NA 2.81E-06 mr1968_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