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Detailed information for vg0915238376:

Variant ID: vg0915238376 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 15238376
Reference Allele: GAlternative Allele: A,GAAAGTAACGGTACACGTTTTGAAAAAAAA
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGGTGGTGAATAAGCTGTGTTCTTTTTTATGGGTTCTCAACCCATCTCTATCGTGCACGTTTTTTTCAAACTGTTAAACGGTACACGTTTTGAAAAAAA[G/A,GAAAGTAACGGTACACGTTTTGAAAAAAAA]
TTTATATATGAAAGTTGCTTTAAAAAATCATATTAATTATTTTTTAAAGTTTTTTTATAGCTAGCACTTAATTAATCACGTGTTAATCTATCGTTCCATT

Reverse complement sequence

AATGGAACGATAGATTAACACGTGATTAATTAAGTGCTAGCTATAAAAAAACTTTAAAAAATAATTAATATGATTTTTTAAAGCAACTTTCATATATAAA[C/T,TTTTTTTTCAAAACGTGTACCGTTACTTTC]
TTTTTTTCAAAACGTGTACCGTTTAACAGTTTGAAAAAAACGTGCACGATAGAGATGGGTTGAGAACCCATAAAAAAGAACACAGCTTATTCACCACCAT

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 95.90% 3.30% 0.74% 0.00% GAAAGTAACGGTACACGTTTTGAAAAAAAA: 0.11%
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 87.80% 9.80% 2.18% 0.00% GAAAGTAACGGTACACGTTTTGAAAAAAAA: 0.26%
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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 0.90% 0.13% 0.00% NA
Tropical Japonica  504 71.80% 23.20% 4.96% 0.00% NA
Japonica Intermediate  241 85.50% 10.00% 2.90% 0.00% GAAAGTAACGGTACACGTTTTGAAAAAAAA: 1.66%
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 5.60% 2.22% 0.00% GAAAGTAACGGTACACGTTTTGAAAAAAAA: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0915238376 G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA LOC_Os09g25420.1 upstream_gene_variant ; 553.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA LOC_Os09g25410.1 downstream_gene_variant ; 2373.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA LOC_Os09g25430.1 downstream_gene_variant ; 2069.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA LOC_Os09g25410.2 downstream_gene_variant ; 2373.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> GAAAGTAACGGTACACGTTTTGAAAAAAAA LOC_Os09g25420-LOC_Os09g25430 intergenic_region ; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> A LOC_Os09g25420.1 upstream_gene_variant ; 552.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> A LOC_Os09g25410.1 downstream_gene_variant ; 2372.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> A LOC_Os09g25430.1 downstream_gene_variant ; 2070.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> A LOC_Os09g25410.2 downstream_gene_variant ; 2372.0bp to feature; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N
vg0915238376 G -> A LOC_Os09g25420-LOC_Os09g25430 intergenic_region ; MODIFIER silent_mutation Average:69.325; most accessible tissue: Zhenshan97 flower, score: 82.481 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915238376 NA 6.20E-07 mr1205 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
vg0915238376 NA 6.25E-08 mr1206 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
vg0915238376 NA 1.93E-06 mr1596 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
vg0915238376 4.82E-06 4.82E-06 mr1663 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
vg0915238376 NA 1.29E-08 mr1668 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
vg0915238376 NA 5.70E-06 mr1668_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