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Detailed information for vg1014019486:

Variant ID: vg1014019486 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14019486
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGTGCAGGTTTTTCCCTAGAATAAATTAATGGTGGGATTTTATTAATTAATCGGCACCGAATTTTTAATTAACCGACATCTATAATAAATTAATGGTGC[G/A]
AGTTTTTTTAAAACAACTGGCATCTATAGCATGGGTGCCGGTTTTTCCCTAGAACCGCACCTATTTCTTCACAAAGGTGCCGGTTTTAGTTGATGGTGCT

Reverse complement sequence

AGCACCATCAACTAAAACCGGCACCTTTGTGAAGAAATAGGTGCGGTTCTAGGGAAAAACCGGCACCCATGCTATAGATGCCAGTTGTTTTAAAAAAACT[C/T]
GCACCATTAATTTATTATAGATGTCGGTTAATTAAAAATTCGGTGCCGATTAATTAATAAAATCCCACCATTAATTTATTCTAGGGAAAAACCTGCACCC

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 81.70% 3.90% 10.54% 3.87% NA
All Indica  2759 69.00% 6.60% 17.87% 6.60% 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 53.10% 5.40% 34.96% 6.55% NA
Indica II  465 77.20% 5.20% 12.04% 5.59% NA
Indica III  913 73.80% 8.80% 10.95% 6.46% NA
Indica Intermediate  786 70.50% 5.70% 16.41% 7.38% 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 92.20% 1.10% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1014019486 G -> A LOC_Os10g26780-LOC_Os10g26800 intergenic_region ; MODIFIER silent_mutation Average:44.248; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1014019486 G -> DEL N N silent_mutation Average:44.248; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014019486 NA 4.94E-06 mr1446 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
vg1014019486 2.12E-06 NA mr1577 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
vg1014019486 2.93E-06 7.22E-08 mr1577 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
vg1014019486 NA 6.14E-07 mr1734 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
vg1014019486 NA 7.87E-07 mr1780 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
vg1014019486 4.99E-07 7.48E-09 mr1792 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
vg1014019486 4.23E-06 5.54E-08 mr1792 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