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Detailed information for vg0505593631:

Variant ID: vg0505593631 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5593631
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGCCACGTGTGTGCCACGTAGGCTGAAAACCGCTTCAAATCGAGTTAGGGGGTATTTCGTCCGGTTTGTATAGTTGGGGGTGAAGAATATCCGGTTTT[G/A]
TGGTTCAGGGGGGTATTTCGGATGACCGCGATAGTTCGGGGGGTAATTCGTACTTTTTCCTAATATTAAATAAAATTTTGTTTGCTGAAAATAATATAAT

Reverse complement sequence

ATTATATTATTTTCAGCAAACAAAATTTTATTTAATATTAGGAAAAAGTACGAATTACCCCCCGAACTATCGCGGTCATCCGAAATACCCCCCTGAACCA[C/T]
AAAACCGGATATTCTTCACCCCCAACTATACAAACCGGACGAAATACCCCCTAACTCGATTTGAAGCGGTTTTCAGCCTACGTGGCACACACGTGGCGAT

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 98.00% 2.00% 0.00% 0.00% NA
All Indica  2759 96.60% 3.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 94.40% 5.60% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 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 98.90% 1.10% 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
vg0505593631 G -> A LOC_Os05g10260-LOC_Os05g10270 intergenic_region ; MODIFIER silent_mutation Average:33.91; most accessible tissue: Zhenshan97 young leaf, score: 56.533 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0505593631 9.04E-06 NA mr1190 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
vg0505593631 3.53E-06 NA mr1373 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
vg0505593631 4.73E-06 4.73E-06 mr1373 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
vg0505593631 2.45E-07 9.50E-10 mr1697 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
vg0505593631 7.29E-08 7.21E-10 mr1697 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