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Detailed information for vg0905608023:

Variant ID: vg0905608023 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5608023
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGGCGGTGGCGCGTTCTCGTCACTGGCTACGCCTCCTTGATCGGTTAGGGTTTGTGGGGTGGAGTGGTGGCGGCGATGAACCTCGTGTCTTGTGCCGT[T/C]
CCGTCCTCCACCCCTCTTTATATGGCACAGTGTGACGGGGGCCCACCAGCCATTGGGCTGGGCGTCCCCGATCAGGGCGCAGGTCAAGGCCCCCTTGAGC

Reverse complement sequence

GCTCAAGGGGGCCTTGACCTGCGCCCTGATCGGGGACGCCCAGCCCAATGGCTGGTGGGCCCCCGTCACACTGTGCCATATAAAGAGGGGTGGAGGACGG[A/G]
ACGGCACAAGACACGAGGTTCATCGCCGCCACCACTCCACCCCACAAACCCTAACCGATCAAGGAGGCGTAGCCAGTGACGAGAACGCGCCACCGCCGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.20% 11.70% 2.03% 0.00% NA
All Indica  2759 99.60% 0.30% 0.07% 0.00% NA
All Japonica  1512 58.60% 35.60% 5.82% 0.00% NA
Aus  269 98.10% 0.70% 1.12% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.25% 0.00% NA
Temperate Japonica  767 28.30% 64.00% 7.69% 0.00% NA
Tropical Japonica  504 94.60% 1.20% 4.17% 0.00% NA
Japonica Intermediate  241 79.70% 17.00% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 3.33% 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
vg0905608023 T -> C LOC_Os09g10290.1 upstream_gene_variant ; 190.0bp to feature; MODIFIER silent_mutation Average:60.991; most accessible tissue: Zhenshan97 flag leaf, score: 73.822 N N N N
vg0905608023 T -> C LOC_Os09g10300.1 upstream_gene_variant ; 2354.0bp to feature; MODIFIER silent_mutation Average:60.991; most accessible tissue: Zhenshan97 flag leaf, score: 73.822 N N N N
vg0905608023 T -> C LOC_Os09g10290-LOC_Os09g10300 intergenic_region ; MODIFIER silent_mutation Average:60.991; most accessible tissue: Zhenshan97 flag leaf, score: 73.822 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905608023 NA 1.49E-06 mr1401 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
vg0905608023 NA 9.23E-07 mr1424 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
vg0905608023 3.36E-06 NA mr1554 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
vg0905608023 NA 2.40E-06 mr1554 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
vg0905608023 NA 3.29E-07 mr1606 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
vg0905608023 NA 7.61E-06 mr1606 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
vg0905608023 NA 3.04E-06 mr1884 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
vg0905608023 NA 7.37E-08 mr1916 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