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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0922636537:

Variant ID: vg0922636537 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22636537
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTCATTGAAACATTTTTTTCTGAGGGATGAAACATGTGAAACATTCCTCGATAACATGGTGCAACATCGTCCGGCGATTTGCACCAGATCGGACATCC[G/A]
ATCCATAGCAGCCTCCGGTTTATCTGCTATCTATCTGCACATGTACAATAAATAGAAGAGAAGAGCTTCAATCGCAATCGGAATCGGAATCGAGTCCGAG

Reverse complement sequence

CTCGGACTCGATTCCGATTCCGATTGCGATTGAAGCTCTTCTCTTCTATTTATTGTACATGTGCAGATAGATAGCAGATAAACCGGAGGCTGCTATGGAT[C/T]
GGATGTCCGATCTGGTGCAAATCGCCGGACGATGTTGCACCATGTTATCGAGGAATGTTTCACATGTTTCATCCCTCAGAAAAAAATGTTTCAATGAAAA

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 89.40% 10.00% 0.61% 0.00% NA
All Indica  2759 82.00% 16.90% 1.05% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 62.70% 34.50% 2.86% 0.00% NA
Indica II  465 63.40% 35.70% 0.86% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 86.90% 12.10% 1.02% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 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
vg0922636537 G -> A LOC_Os09g39360.1 5_prime_UTR_variant ; 742.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922636537 G -> A LOC_Os09g39350.1 upstream_gene_variant ; 3042.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922636537 G -> A LOC_Os09g39350.2 upstream_gene_variant ; 3042.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0922636537 G -> A LOC_Os09g39370.1 downstream_gene_variant ; 2075.0bp to feature; 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
vg0922636537 NA 1.28E-09 mr1457 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
vg0922636537 5.13E-10 NA mr1865 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
vg0922636537 4.17E-09 2.80E-10 mr1865 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
vg0922636537 NA 2.40E-06 mr1457_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
vg0922636537 6.37E-11 NA mr1865_2 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
vg0922636537 2.27E-10 3.65E-10 mr1865_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