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Detailed information for vg0317301865:

Variant ID: vg0317301865 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17301865
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGCACTAGCAAATGCAAAGTATGAAAAGCACACTTTGTAATTGGATAACTGCCTATCACTTTTGTGATTTTGGAGAGCATGACTAAGTTGCATTACCC[G/A]
AATATAATGCACCGGAGGAGGGTGAAATACCGAAGAATGCAAAGGTATACCTCATATTGTCTAGAGGCCTCGAGAAAAATAATGGGACAAGAACTCCGGC

Reverse complement sequence

GCCGGAGTTCTTGTCCCATTATTTTTCTCGAGGCCTCTAGACAATATGAGGTATACCTTTGCATTCTTCGGTATTTCACCCTCCTCCGGTGCATTATATT[C/T]
GGGTAATGCAACTTAGTCATGCTCTCCAAAATCACAAAAGTGATAGGCAGTTATCCAATTACAAAGTGTGCTTTTCATACTTTGCATTTGCTAGTGCTTG

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 89.50% 10.50% 0.00% 0.00% NA
All Indica  2759 95.50% 4.50% 0.00% 0.00% NA
All Japonica  1512 95.20% 4.80% 0.00% 0.00% NA
Aus  269 20.40% 79.60% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 95.80% 4.20% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 86.50% 13.50% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 19.80% 80.20% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0317301865 G -> A LOC_Os03g30334.1 upstream_gene_variant ; 2451.0bp to feature; MODIFIER silent_mutation Average:42.414; most accessible tissue: Minghui63 flag leaf, score: 59.244 N N N N
vg0317301865 G -> A LOC_Os03g30320.1 downstream_gene_variant ; 2395.0bp to feature; MODIFIER silent_mutation Average:42.414; most accessible tissue: Minghui63 flag leaf, score: 59.244 N N N N
vg0317301865 G -> A LOC_Os03g30320-LOC_Os03g30334 intergenic_region ; MODIFIER silent_mutation Average:42.414; most accessible tissue: Minghui63 flag leaf, score: 59.244 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317301865 NA 5.27E-06 mr1057 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
vg0317301865 NA 1.75E-06 mr1073 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
vg0317301865 NA 1.46E-08 mr1153 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
vg0317301865 NA 3.32E-08 mr1262 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
vg0317301865 NA 3.58E-08 mr1403 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
vg0317301865 NA 1.90E-06 mr1417 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
vg0317301865 NA 3.44E-08 mr1465 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
vg0317301865 NA 4.15E-12 mr1522 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
vg0317301865 NA 1.31E-11 mr1612 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
vg0317301865 NA 2.02E-06 mr1652 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
vg0317301865 NA 1.91E-07 mr1989 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
vg0317301865 NA 8.10E-07 mr1126_2 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
vg0317301865 NA 2.84E-08 mr1612_2 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