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Detailed information for vg1127840259:

Variant ID: vg1127840259 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27840259
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:


AACGAAGAGAGTATGTAGCTACATTTTAAGGCTGAGGAAGCGTTTTTAACATTCCCACTCGAGAAACTCATGTTAGCTAAACATTAGAAAACCCCATGCT[T/C]
TATGGTCAAAGTTGCATAAAACCCAAAATATCATCACCAGTGTCACATTACTCTAGGTTTTATGGTTCTAAAGTTTTACAATACCCCACCCTATATGTGT

Reverse complement sequence

ACACATATAGGGTGGGGTATTGTAAAACTTTAGAACCATAAAACCTAGAGTAATGTGACACTGGTGATGATATTTTGGGTTTTATGCAACTTTGACCATA[A/G]
AGCATGGGGTTTTCTAATGTTTAGCTAACATGAGTTTCTCGAGTGGGAATGTTAAAAACGCTTCCTCAGCCTTAAAATGTAGCTACATACTCTCTTCGTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.30% 25.30% 17.18% 3.24% NA
All Indica  2759 49.10% 34.00% 13.56% 3.37% NA
All Japonica  1512 63.90% 9.90% 22.75% 3.44% NA
Aus  269 59.90% 23.40% 14.50% 2.23% NA
Indica I  595 32.40% 38.70% 22.18% 6.72% NA
Indica II  465 52.70% 31.80% 14.84% 0.65% NA
Indica III  913 58.70% 31.70% 7.67% 1.97% NA
Indica Intermediate  786 48.30% 34.50% 13.10% 4.07% NA
Temperate Japonica  767 50.30% 14.90% 30.77% 4.04% NA
Tropical Japonica  504 83.50% 3.40% 11.11% 1.98% NA
Japonica Intermediate  241 66.00% 7.90% 21.58% 4.56% NA
VI/Aromatic  96 27.10% 37.50% 34.38% 1.04% NA
Intermediate  90 64.40% 10.00% 24.44% 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
vg1127840259 T -> DEL N N silent_mutation Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1127840259 T -> C LOC_Os11g46000.1 upstream_gene_variant ; 1254.0bp to feature; MODIFIER silent_mutation Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1127840259 T -> C LOC_Os11g46000.2 upstream_gene_variant ; 1254.0bp to feature; MODIFIER silent_mutation Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1127840259 T -> C LOC_Os11g46000.3 upstream_gene_variant ; 1785.0bp to feature; MODIFIER silent_mutation Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1127840259 T -> C LOC_Os11g45990-LOC_Os11g46000 intergenic_region ; MODIFIER silent_mutation Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127840259 1.47E-06 2.00E-06 mr1337 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
vg1127840259 5.48E-06 5.46E-06 mr1429 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