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Detailed information for vg0500663064:

Variant ID: vg0500663064 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 663064
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGAGTACGTGTATACGCTCATAGAGGGTGAGTGTGAGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTATGACTTATGAGTGTGTC[G/A]
GAGGATGAACTCCTCCGGCGGGGGACCATGAGAGCACTCCTTTTTTGGTTCGGCCGGGGGCAACAGGTGGAGGTCGAGGAACTGGAAAGATTGGGAGAAA

Reverse complement sequence

TTTCTCCCAATCTTTCCAGTTCCTCGACCTCCACCTGTTGCCCCCGGCCGAACCAAAAAAGGAGTGCTCTCATGGTCCCCCGCCGGAGGAGTTCATCCTC[C/T]
GACACACTCATAAGTCATAACACACACACACACACACACACACACACACACACACACACTCACTCACACTCACCCTCTATGAGCGTATACACGTACTCCT

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 97.40% 2.60% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.10% 7.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 78.80% 21.00% 0.20% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0500663064 G -> A LOC_Os05g02150.1 upstream_gene_variant ; 2809.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500663064 G -> A LOC_Os05g02150-LOC_Os05g02160 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500663064 NA 7.06E-06 mr1657 Jap_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
vg0500663064 NA 3.07E-06 mr1890 Jap_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
vg0500663064 3.44E-06 3.44E-06 mr1891 Jap_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
vg0500663064 8.98E-06 8.98E-06 mr1918 Jap_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
vg0500663064 NA 6.72E-06 mr1738_2 Jap_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