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Detailed information for vg0418069807:

Variant ID: vg0418069807 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18069807
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, A: 0.24, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTGTGGTGGCATGGCACGGATCGAGGCACTTAGCAGCAGCACGGTGCGGATTGAGGCACACGGTGATGGCGCCTGGCAGATGCTTGGTGCGGAGGGAC[T/A]
TCTCTATGACAGTGGGTGCATATTTTACTCTATGGCGTGCAAATGGACTCCATTTTGTTTCTGATATATTTATCTTGTTCTTTCCCTTTGATGCATGCAA

Reverse complement sequence

TTGCATGCATCAAAGGGAAAGAACAAGATAAATATATCAGAAACAAAATGGAGTCCATTTGCACGCCATAGAGTAAAATATGCACCCACTGTCATAGAGA[A/T]
GTCCCTCCGCACCAAGCATCTGCCAGGCGCCATCACCGTGTGCCTCAATCCGCACCGTGCTGCTGCTAAGTGCCTCGATCCGTGCCATGCCACCACAGCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.80% 39.00% 0.74% 16.50% NA
All Indica  2759 69.00% 20.00% 0.87% 10.15% NA
All Japonica  1512 0.90% 68.00% 0.46% 30.69% NA
Aus  269 44.60% 50.60% 1.12% 3.72% NA
Indica I  595 62.20% 36.30% 1.01% 0.50% NA
Indica II  465 53.80% 38.30% 0.86% 7.10% NA
Indica III  913 77.80% 1.80% 0.66% 19.82% NA
Indica Intermediate  786 72.90% 18.10% 1.02% 8.02% NA
Temperate Japonica  767 0.30% 97.40% 0.13% 2.22% NA
Tropical Japonica  504 1.20% 35.70% 0.79% 62.30% NA
Japonica Intermediate  241 2.10% 41.90% 0.83% 55.19% NA
VI/Aromatic  96 11.50% 72.90% 0.00% 15.62% NA
Intermediate  90 25.60% 61.10% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0418069807 T -> DEL N N silent_mutation Average:61.994; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg0418069807 T -> A LOC_Os04g30270.1 intron_variant ; MODIFIER silent_mutation Average:61.994; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418069807 NA 6.57E-08 mr1851 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
vg0418069807 2.11E-06 5.92E-09 mr1851 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
vg0418069807 4.06E-06 2.20E-07 mr1864 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
vg0418069807 NA 9.10E-08 mr1042_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
vg0418069807 9.35E-07 1.53E-08 mr1680_2 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
vg0418069807 NA 7.17E-09 mr1742_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