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Detailed information for vg0328403714:

Variant ID: vg0328403714 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28403714
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAGAGATTTTGAGTTCGAATCCCACATATTATTTTTTATTTAGTATGTATCGTTATTACCAGTTCTTTTAATCAGTACTAAAGATCGAGATTTTTAGT[A/C]
TTAATTTACATCGTTCTCGGTTGTTACAACCAGTAATAAAGAGGGTTATTAACCGGTAATAAAAATGAGTTCTCCGGTAGTGTTTGAACCGTTGTGGATG

Reverse complement sequence

CATCCACAACGGTTCAAACACTACCGGAGAACTCATTTTTATTACCGGTTAATAACCCTCTTTATTACTGGTTGTAACAACCGAGAACGATGTAAATTAA[T/G]
ACTAAAAATCTCGATCTTTAGTACTGATTAAAAGAACTGGTAATAACGATACATACTAAATAAAAAATAATATGTGGGATTCGAACTCAAAATCTCTCAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.50% 4.80% 1.63% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 80.10% 14.90% 5.03% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 63.00% 28.30% 8.74% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 94.20% 2.50% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg0328403714 A -> C LOC_Os03g49850.1 upstream_gene_variant ; 4071.0bp to feature; MODIFIER silent_mutation Average:54.865; most accessible tissue: Callus, score: 85.094 N N N N
vg0328403714 A -> C LOC_Os03g49840.1 downstream_gene_variant ; 3486.0bp to feature; MODIFIER silent_mutation Average:54.865; most accessible tissue: Callus, score: 85.094 N N N N
vg0328403714 A -> C LOC_Os03g49840-LOC_Os03g49850 intergenic_region ; MODIFIER silent_mutation Average:54.865; most accessible tissue: Callus, score: 85.094 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328403714 NA 1.57E-06 mr1310 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
vg0328403714 4.15E-07 1.73E-08 mr1926 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
vg0328403714 1.37E-06 1.62E-08 mr1310_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
vg0328403714 5.44E-06 5.26E-08 mr1959_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