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Detailed information for vg0417784069:

Variant ID: vg0417784069 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17784069
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:


CATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTCGCAACCTGGGTACAACGACGTTCTGTGGTCCTCTAACATCTTGTCCAATTTAT[G/A]
GGCCCCTTTTCACTTTCGTAGTCCTCCTTGGCGTCCTGCAACATCTGACCAAGATCATCTGCAACGTCGTTACCATCAGCATCCCTTTCCTCCTCGCCCG

Reverse complement sequence

CGGGCGAGGAGGAAAGGGATGCTGATGGTAACGACGTTGCAGATGATCTTGGTCAGATGTTGCAGGACGCCAAGGAGGACTACGAAAGTGAAAAGGGGCC[C/T]
ATAAATTGGACAAGATGTTAGAGGACCACAGAACGTCGTTGTACCCAGGTTGCGAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.10% 7.90% 20.99% 46.95% NA
All Indica  2759 31.40% 5.90% 27.62% 35.09% NA
All Japonica  1512 6.00% 9.60% 5.62% 78.84% NA
Aus  269 57.20% 4.50% 37.55% 0.74% NA
Indica I  595 54.80% 8.20% 9.24% 27.73% NA
Indica II  465 10.80% 6.50% 29.89% 52.90% NA
Indica III  913 24.30% 5.50% 39.98% 30.23% NA
Indica Intermediate  786 34.00% 4.50% 25.83% 35.75% NA
Temperate Japonica  767 2.50% 8.60% 2.48% 86.44% NA
Tropical Japonica  504 11.30% 13.10% 9.92% 65.67% NA
Japonica Intermediate  241 5.80% 5.40% 6.64% 82.16% NA
VI/Aromatic  96 14.60% 41.70% 28.12% 15.62% NA
Intermediate  90 20.00% 14.40% 18.89% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0417784069 G -> DEL N N silent_mutation Average:7.494; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0417784069 G -> A LOC_Os04g29830.1 intron_variant ; MODIFIER silent_mutation Average:7.494; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417784069 7.67E-06 NA mr1319 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
vg0417784069 NA 6.50E-06 mr1367 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
vg0417784069 8.52E-06 3.03E-07 mr1603 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
vg0417784069 7.72E-06 NA mr1789 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
vg0417784069 4.55E-06 NA mr1864 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
vg0417784069 NA 4.43E-06 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
vg0417784069 NA 7.59E-08 mr1904 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