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Detailed information for vg1005802057:

Variant ID: vg1005802057 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5802057
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


CACCATCTACATCACTTAGTGGCTCGAAGGCGGCGCAAACTTGTTGAAAAGCCTTCCTAAGATTCTCCATCTTCCTCCCTTGGTTAGAACCCTTCGACTT[G/A]
TTGTAGTTGGGCTTGTTGTTGTTGGTCTTCTCACCATCTTTGTCTTCTCTTTTGCCTCTCCCAAGCTTAGGACAATGCGAACGAAGATGATCAATTGAAC

Reverse complement sequence

GTTCAATTGATCATCTTCGTTCGCATTGTCCTAAGCTTGGGAGAGGCAAAAGAGAAGACAAAGATGGTGAGAAGACCAACAACAACAAGCCCAACTACAA[C/T]
AAGTCGAAGGGTTCTAACCAAGGGAGGAAGATGGAGAATCTTAGGAAGGCTTTTCAACAAGTTTGCGCCGCCTTCGAGCCACTAAGTGATGTAGATGGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.40% 7.40% 5.40% 2.77% NA
All Indica  2759 74.00% 12.20% 9.10% 4.68% NA
All Japonica  1512 99.60% 0.30% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.40% 4.00% 3.70% 0.84% NA
Indica II  465 71.20% 9.20% 11.83% 7.74% NA
Indica III  913 69.30% 15.00% 9.64% 6.02% NA
Indica Intermediate  786 67.90% 16.90% 10.94% 4.20% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 88.90% 5.60% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005802057 G -> A LOC_Os10g10520.1 synonymous_variant ; p.Asn315Asn; LOW synonymous_codon Average:20.52; most accessible tissue: Zhenshan97 root, score: 27.411 N N N N
vg1005802057 G -> DEL LOC_Os10g10520.1 N frameshift_variant Average:20.52; most accessible tissue: Zhenshan97 root, score: 27.411 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005802057 9.38E-06 2.05E-11 mr1027_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
vg1005802057 NA 7.80E-06 mr1057_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
vg1005802057 1.09E-06 8.58E-12 mr1580_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
vg1005802057 2.43E-06 6.81E-08 mr1790_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
vg1005802057 1.11E-06 4.69E-12 mr1825_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
vg1005802057 NA 2.50E-06 mr1943_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