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Detailed information for vg0111893625:

Variant ID: vg0111893625 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11893625
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CTCAATTTGTTGCCCAGTCTGATTGTTGTCCTTGAACCACAAAACCGGATACAACGCAACCCCCCAACTTACAAAACCAATGCACATAAGGTCCTAAGGC[G/A]
GTTTGGATAGCGGTTTTGGCTGACGTGGCGCCTACGTGACTGGTTTGACTAGGTCTCCGTCCCACCTGGTAGTGACGTGGCGCTTACGTGGCAATCATAT

Reverse complement sequence

ATATGATTGCCACGTAAGCGCCACGTCACTACCAGGTGGGACGGAGACCTAGTCAAACCAGTCACGTAGGCGCCACGTCAGCCAAAACCGCTATCCAAAC[C/T]
GCCTTAGGACCTTATGTGCATTGGTTTTGTAAGTTGGGGGGTTGCGTTGTATCCGGTTTTGTGGTTCAAGGACAACAATCAGACTGGGCAACAAATTGAG

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 90.40% 9.60% 0.00% 0.00% NA
All Indica  2759 83.60% 16.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 65.70% 34.30% 0.00% 0.00% NA
Indica Intermediate  786 85.90% 14.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0111893625 G -> A LOC_Os01g21300.1 upstream_gene_variant ; 3933.0bp to feature; MODIFIER silent_mutation Average:70.541; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0111893625 G -> A LOC_Os01g21290.1 downstream_gene_variant ; 3567.0bp to feature; MODIFIER silent_mutation Average:70.541; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0111893625 G -> A LOC_Os01g21290-LOC_Os01g21300 intergenic_region ; MODIFIER silent_mutation Average:70.541; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111893625 4.23E-06 6.21E-06 mr1305 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
vg0111893625 NA 7.81E-06 mr1667 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
vg0111893625 NA 3.82E-06 mr1533_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