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Detailed information for vg0205949832:

Variant ID: vg0205949832 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5949832
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGGGTCCGATTGAGATAGATTCATCCGTGACGGTCGTTTGCCCGATTGAGATAACTCTTCACATCTGTGACTTGTAGCCTGTGACGGACGCCATGCCC[G/A]
ATTGAGATGGGGCTTACCGCCCGATTGAGATGATGGTATCCGTTCTAGTGAGTTACACTGGTGGAGAAGTGCTTTTTAGTCCCGGTTTGTAACCCTCCTG

Reverse complement sequence

CAGGAGGGTTACAAACCGGGACTAAAAAGCACTTCTCCACCAGTGTAACTCACTAGAACGGATACCATCATCTCAATCGGGCGGTAAGCCCCATCTCAAT[C/T]
GGGCATGGCGTCCGTCACAGGCTACAAGTCACAGATGTGAAGAGTTATCTCAATCGGGCAAACGACCGTCACGGATGAATCTATCTCAATCGGACCCTAA

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 73.80% 26.20% 0.06% 0.00% NA
All Indica  2759 57.40% 42.50% 0.11% 0.00% NA
All Japonica  1512 98.10% 1.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.60% 32.40% 0.00% 0.00% NA
Indica II  465 61.90% 37.80% 0.22% 0.00% NA
Indica III  913 49.40% 50.50% 0.11% 0.00% NA
Indica Intermediate  786 56.40% 43.50% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 2.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0205949832 G -> A LOC_Os02g11100.1 upstream_gene_variant ; 2487.0bp to feature; MODIFIER silent_mutation Average:54.65; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0205949832 G -> A LOC_Os02g11090.1 downstream_gene_variant ; 3509.0bp to feature; MODIFIER silent_mutation Average:54.65; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0205949832 G -> A LOC_Os02g11090-LOC_Os02g11100 intergenic_region ; MODIFIER silent_mutation Average:54.65; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205949832 NA 8.12E-13 mr1170 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
vg0205949832 NA 7.28E-07 mr1170 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
vg0205949832 3.21E-08 5.96E-13 mr1170_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
vg0205949832 8.55E-07 6.66E-10 mr1170_2 Ind_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