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Detailed information for vg0502963065:

Variant ID: vg0502963065 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2963065
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGACAACCAACCTCCATTGCCACTGGCTGAACCCCTGGCGGCTGATGCTGGAGCGAAGGAGAGAGCGGACGCGGGAGCTGACACGAGAACGGGAGCT[G/A]
GAGCTGGTGCTGGAGCTGCAGGAACTACCGGAGCTGCGGGCGGAACTGGAGGTGCTGCGGGAGCTGCTGATGGAGGTGGGTTCCTGGGCGCAAGCTGGAT

Reverse complement sequence

ATCCAGCTTGCGCCCAGGAACCCACCTCCATCAGCAGCTCCCGCAGCACCTCCAGTTCCGCCCGCAGCTCCGGTAGTTCCTGCAGCTCCAGCACCAGCTC[C/T]
AGCTCCCGTTCTCGTGTCAGCTCCCGCGTCCGCTCTCTCCTTCGCTCCAGCATCAGCCGCCAGGGGTTCAGCCAGTGGCAATGGAGGTTGGTTGTCTGCT

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 99.20% 0.50% 0.38% 0.00% NA
All Indica  2759 98.60% 0.80% 0.65% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.50% 1.50% 2.02% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.00% 0.80% 0.22% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0502963065 G -> A LOC_Os05g05900.1 missense_variant ; p.Pro232Leu; MODERATE N Average:58.175; most accessible tissue: Minghui63 flag leaf, score: 84.028 N N N N
vg0502963065 G -> A LOC_Os05g05890.1 upstream_gene_variant ; 518.0bp to feature; MODIFIER N Average:58.175; most accessible tissue: Minghui63 flag leaf, score: 84.028 N N N N
vg0502963065 G -> A LOC_Os05g05910.1 upstream_gene_variant ; 1461.0bp to feature; MODIFIER N Average:58.175; most accessible tissue: Minghui63 flag leaf, score: 84.028 N N N N
vg0502963065 G -> A LOC_Os05g05920.1 upstream_gene_variant ; 4511.0bp to feature; MODIFIER N Average:58.175; most accessible tissue: Minghui63 flag leaf, score: 84.028 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502963065 NA 1.91E-15 mr1201 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
vg0502963065 NA 1.24E-11 mr1219 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
vg0502963065 NA 2.76E-12 mr1274 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
vg0502963065 NA 5.11E-14 mr1201_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
vg0502963065 NA 6.05E-11 mr1219_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
vg0502963065 NA 6.72E-13 mr1274_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