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Search for Variation information by Variation ID:

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

Detailed information for vg0105869431:

Variant ID: vg0105869431 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5869431
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, C: 0.26, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTTAGCGCAAAGGGGGTTGAGAGGAGGCTTATTCACTCGCACCCCCACTCACCCCGTCCCTATCTCTCTTACCCTTTCAGCCTCTCCTCCCCTCC[G/C]
CTTGCCCCCTCTCCTCCACTCCACCTCTCCTCTCCGCGGCTCCCTCTCCATCGCCTGAGATGATGGCGAGAGCGGACGGAGCTGCATCCAGCAGTGGCGG

Reverse complement sequence

CCGCCACTGCTGGATGCAGCTCCGTCCGCTCTCGCCATCATCTCAGGCGATGGAGAGGGAGCCGCGGAGAGGAGAGGTGGAGTGGAGGAGAGGGGGCAAG[C/G]
GGAGGGGAGGAGAGGCTGAAAGGGTAAGAGAGATAGGGACGGGGTGAGTGGGGGTGCGAGTGAATAAGCCTCCTCTCAACCCCCTTTGCGCTAAAAAAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.70% 24.30% 0.00% 0.00% NA
All Indica  2759 69.10% 30.90% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 5.60% 94.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 60.40% 39.60% 0.00% 0.00% NA
Indica III  913 46.10% 53.90% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 22.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 0.00% 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
vg0105869431 G -> C LOC_Os01g11000.1 missense_variant ; p.Arg18Gly; MODERATE nonsynonymous_codon ; R18G Average:63.335; most accessible tissue: Zhenshan97 young leaf, score: 77.736 unknown unknown TOLERATED 0.15

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105869431 NA 3.70E-06 mr1236 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
vg0105869431 NA 3.49E-06 mr1496 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
vg0105869431 1.93E-07 2.48E-13 mr1498 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
vg0105869431 6.75E-06 NA mr1769 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
vg0105869431 8.41E-07 1.42E-13 mr1769 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
vg0105869431 5.72E-07 NA mr1951 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
vg0105869431 4.55E-08 2.41E-12 mr1951 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
vg0105869431 NA 2.09E-07 mr1582_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
vg0105869431 NA 3.60E-09 mr1769_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