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Detailed information for vg1203995948:

Variant ID: vg1203995948 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3995948
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTAGAGCTCTAACCCATCGATAGCAGCATGTCAGATAAGGGACTTGGTGCTTGGAGGTTTCGCCGAGATTACCACAGGAGGTGGTTTCTCCAATGAAG[A/G]
TTGGCTTGGGAGGCCCAACCCAGCCGACATTCATCTTCTTTCAAGTCGGAAGCATCACCTTTCTAGTCCTCGTTATTTCACCGCCTCTTTTAACTACTCG

Reverse complement sequence

CGAGTAGTTAAAAGAGGCGGTGAAATAACGAGGACTAGAAAGGTGATGCTTCCGACTTGAAAGAAGATGAATGTCGGCTGGGTTGGGCCTCCCAAGCCAA[T/C]
CTTCATTGGAGAAACCACCTCCTGTGGTAATCTCGGCGAAACCTCCAAGCACCAAGTCCCTTATCTGACATGCTGCTATCGATGGGTTAGAGCTCTAGGA

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 65.10% 34.70% 0.15% 0.00% NA
All Indica  2759 93.70% 6.20% 0.07% 0.00% NA
All Japonica  1512 13.40% 86.50% 0.13% 0.00% NA
Aus  269 90.70% 8.60% 0.74% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 82.80% 17.00% 0.22% 0.00% NA
Indica III  913 96.40% 3.60% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 7.00% 0.13% 0.00% NA
Temperate Japonica  767 4.80% 95.00% 0.13% 0.00% NA
Tropical Japonica  504 17.10% 82.90% 0.00% 0.00% NA
Japonica Intermediate  241 32.80% 66.80% 0.41% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 34.40% 64.40% 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
vg1203995948 A -> G LOC_Os12g07880.1 upstream_gene_variant ; 1450.0bp to feature; MODIFIER silent_mutation Average:58.438; most accessible tissue: Callus, score: 87.52 N N N N
vg1203995948 A -> G LOC_Os12g07890.1 upstream_gene_variant ; 4202.0bp to feature; MODIFIER silent_mutation Average:58.438; most accessible tissue: Callus, score: 87.52 N N N N
vg1203995948 A -> G LOC_Os12g07880-LOC_Os12g07890 intergenic_region ; MODIFIER silent_mutation Average:58.438; most accessible tissue: Callus, score: 87.52 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203995948 NA 5.89E-07 mr1691 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
vg1203995948 3.79E-07 1.80E-10 mr1693 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
vg1203995948 NA 7.18E-07 mr1720 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
vg1203995948 5.80E-06 5.15E-07 mr1679_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
vg1203995948 4.17E-07 6.08E-10 mr1691_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
vg1203995948 2.75E-07 2.00E-09 mr1720_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