Search for Variation information by Variation ID:

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

Detailed information for vg0801635012:

Variant ID: vg0801635012 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1635012
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.06, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GCGACCTCGAGTCGTCGGCGTTCGTCCGCGACGACCGCCTCATCGTCGAGTGCGTCATCGACGTCGTCGTCGCCAACGGCGGCGACGACGACACGGCGGC[C/G]
GCGGCGTCCCCCCTCGCCGGCGTGCCGGCGCCGGACCTGTCGAGGCACCTCGGCGAGCTGCTGGAGCGGGCGGACGGCGTGGGCGCGGACGTCACGTTCG

Reverse complement sequence

CGAACGTGACGTCCGCGCCCACGCCGTCCGCCCGCTCCAGCAGCTCGCCGAGGTGCCTCGACAGGTCCGGCGCCGGCACGCCGGCGAGGGGGGACGCCGC[G/C]
GCCGCCGTGTCGTCGTCGCCGCCGTTGGCGACGACGACGTCGATGACGCACTCGACGATGAGGCGGTCGTCGCGGACGAACGCCGACGACTCGAGGTCGC

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 72.90% 26.20% 0.13% 0.78% NA
All Indica  2759 54.60% 43.80% 0.22% 1.34% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 68.70% 28.40% 0.34% 2.52% NA
Indica II  465 81.10% 18.90% 0.00% 0.00% NA
Indica III  913 28.80% 70.30% 0.11% 0.77% NA
Indica Intermediate  786 58.30% 39.40% 0.38% 1.91% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg0801635012 C -> G LOC_Os08g03490.1 synonymous_variant ; p.Ala170Ala; LOW synonymous_codon Average:75.028; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N
vg0801635012 C -> DEL LOC_Os08g03490.1 N frameshift_variant Average:75.028; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801635012 NA 2.92E-11 mr1739 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
vg0801635012 NA 4.21E-09 mr1739 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
vg0801635012 NA 8.35E-06 mr1751 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
vg0801635012 NA 7.94E-06 mr1277_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