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Detailed information for vg0920511311:

Variant ID: vg0920511311 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20511311
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCCTTTTTGAGAGAGGAGAACCAATTTTTATCACCGGTCATGTGCCGCGAACAACTGGAATCCACGATCCACACATTCTCCTTCCTTGCCACCAAAGC[G/C]
TACACACAAGCAGAAGTCGAAGCCTCAGTACTGGGGTTAGAAGATAATAAAAATTTAGGAATCCAGTACTGAGACACACGACCAGAAGATCCAACAGGCA

Reverse complement sequence

TGCCTGTTGGATCTTCTGGTCGTGTGTCTCAGTACTGGATTCCTAAATTTTTATTATCTTCTAACCCCAGTACTGAGGCTTCGACTTCTGCTTGTGTGTA[C/G]
GCTTTGGTGGCAAGGAAGGAGAATGTGTGGATCGTGGATTCCAGTTGTTCGCGGCACATGACCGGTGATAAAAATTGGTTCTCCTCTCTCAAAAAGGCAT

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 44.30% 7.30% 32.46% 15.89% NA
All Indica  2759 15.30% 8.50% 49.26% 27.00% NA
All Japonica  1512 99.60% 0.00% 0.33% 0.07% NA
Aus  269 4.80% 41.30% 53.90% 0.00% NA
Indica I  595 17.30% 15.60% 22.86% 44.20% NA
Indica II  465 8.40% 4.30% 68.17% 19.14% NA
Indica III  913 13.50% 8.70% 56.63% 21.25% NA
Indica Intermediate  786 19.80% 5.30% 49.49% 25.32% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 1.24% 0.41% NA
VI/Aromatic  96 92.70% 0.00% 6.25% 1.04% NA
Intermediate  90 73.30% 1.10% 21.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920511311 G -> DEL LOC_Os09g35660.1 N frameshift_variant Average:32.981; most accessible tissue: Zhenshan97 root, score: 54.262 N N N N
vg0920511311 G -> C LOC_Os09g35660.1 stop_gained ; p.Tyr518*; HIGH stop_gained Average:32.981; most accessible tissue: Zhenshan97 root, score: 54.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920511311 NA 1.66E-08 mr1302 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
vg0920511311 NA 4.76E-08 mr1488 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
vg0920511311 NA 1.21E-08 mr1506 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
vg0920511311 NA 2.39E-19 mr1518 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
vg0920511311 NA 2.19E-11 mr1623 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
vg0920511311 NA 2.98E-21 mr1676 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
vg0920511311 NA 2.81E-06 mr1676 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
vg0920511311 NA 7.38E-07 mr1797 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
vg0920511311 NA 7.38E-07 mr1801 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
vg0920511311 NA 4.81E-24 mr1676_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
vg0920511311 NA 4.08E-07 mr1676_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