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Detailed information for vg0314646110:

Variant ID: vg0314646110 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14646110
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.28, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


CGAAGATCGCCAGTGCCGCGAGGTGGAGGGGTAGCTTGTTGAGGTGATTCCCTCCGTTCCGGATCTTCACCATTGGCCTCTCCAGTTGGTGGCTGCTCCT[A/G]
GTGTGCTGCGGTAGCGGCTTCTTCAAACGCGTTGCTGAGGTTAGTCACTGATTCCCGTAGTCGTTATGTCCAACGCTCGAGGTCAACGTTCAGAATGGGA

Reverse complement sequence

TCCCATTCTGAACGTTGACCTCGAGCGTTGGACATAACGACTACGGGAATCAGTGACTAACCTCAGCAACGCGTTTGAAGAAGCCGCTACCGCAGCACAC[T/C]
AGGAGCAGCCACCAACTGGAGAGGCCAATGGTGAAGATCCGGAACGGAGGGAATCACCTCAACAAGCTACCCCTCCACCTCGCGGCACTGGCGATCTTCG

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 54.50% 44.70% 0.85% 0.02% NA
All Indica  2759 81.40% 17.20% 1.30% 0.04% NA
All Japonica  1512 1.20% 98.80% 0.00% 0.00% NA
Aus  269 96.30% 3.00% 0.74% 0.00% NA
Indica I  595 89.90% 7.70% 2.35% 0.00% NA
Indica II  465 90.80% 7.30% 1.94% 0.00% NA
Indica III  913 72.20% 27.30% 0.44% 0.11% NA
Indica Intermediate  786 80.30% 18.60% 1.15% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 44.40% 53.30% 2.22% 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
vg0314646110 A -> DEL N N silent_mutation Average:41.358; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0314646110 A -> G LOC_Os03g25590.1 intron_variant ; MODIFIER silent_mutation Average:41.358; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314646110 NA 1.48E-06 mr1104 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
vg0314646110 NA 1.93E-06 mr1107 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
vg0314646110 NA 3.58E-07 mr1213 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
vg0314646110 NA 2.81E-14 mr1218 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
vg0314646110 NA 5.27E-06 mr1246 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
vg0314646110 NA 6.50E-06 mr1437 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
vg0314646110 NA 1.70E-06 mr1850 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
vg0314646110 NA 4.82E-36 mr1155_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
vg0314646110 NA 5.44E-15 mr1216_2 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
vg0314646110 NA 5.10E-06 mr1216_2 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