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Detailed information for vg1011760237:

Variant ID: vg1011760237 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11760237
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.55, T: 0.45, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


CGTGCGGTCGACTTAAGAGGACCGCACGGAAAAATCAATTTTCGCGTGCGGGCATATTAAGTGGACCGCACGCGAAAATACATCTCCCTCTCACTCACTT[T/C]
AAAATTTTCACACCTCTCCCTCTTACTCACTTCAAAATTTTCACACATCTCCCTCTAACTCATTTCAATTTTTTCACACCTCCTCTCCCTTCCTTTTTGT

Reverse complement sequence

ACAAAAAGGAAGGGAGAGGAGGTGTGAAAAAATTGAAATGAGTTAGAGGGAGATGTGTGAAAATTTTGAAGTGAGTAAGAGGGAGAGGTGTGAAAATTTT[A/G]
AAGTGAGTGAGAGGGAGATGTATTTTCGCGTGCGGTCCACTTAATATGCCCGCACGCGAAAATTGATTTTTCCGTGCGGTCCTCTTAAGTCGACCGCACG

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 90.80% 9.20% 0.02% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 72.70% 27.20% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 57.40% 42.50% 0.13% 0.00% NA
Tropical Japonica  504 90.50% 9.50% 0.00% 0.00% NA
Japonica Intermediate  241 84.20% 15.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1011760237 T -> C LOC_Os10g22640.1 upstream_gene_variant ; 4767.0bp to feature; MODIFIER silent_mutation Average:66.861; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg1011760237 T -> C LOC_Os10g22630.1 downstream_gene_variant ; 997.0bp to feature; MODIFIER silent_mutation Average:66.861; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg1011760237 T -> C LOC_Os10g22630.2 downstream_gene_variant ; 1059.0bp to feature; MODIFIER silent_mutation Average:66.861; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N
vg1011760237 T -> C LOC_Os10g22630-LOC_Os10g22640 intergenic_region ; MODIFIER silent_mutation Average:66.861; most accessible tissue: Minghui63 young leaf, score: 82.907 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011760237 NA 6.99E-06 mr1096 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
vg1011760237 1.06E-06 NA mr1746 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