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Detailed information for vg0335957254:

Variant ID: vg0335957254 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 35957254
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGAAGCTTTGCAGGAACTCCTGACGATTCCACATCCACCTTCCAAGGTGATTCTCTCCTGTTAATGGAAGATGTTTAGAGAGTAAACATTAACTAGC[G/A]
TTTATTCATTTGCAAGTTCAGGAAACCATGTGCCTCAATTGAAAAGTGCCAACCTACCGTGGTACAGCATGTTTTGTGTTATACATCGGCTCAGCCGTTT

Reverse complement sequence

AAACGGCTGAGCCGATGTATAACACAAAACATGCTGTACCACGGTAGGTTGGCACTTTTCAATTGAGGCACATGGTTTCCTGAACTTGCAAATGAATAAA[C/T]
GCTAGTTAATGTTTACTCTCTAAACATCTTCCATTAACAGGAGAGAATCACCTTGGAAGGTGGATGTGGAATCGTCAGGAGTTCCTGCAAAGCTTCAACT

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 95.40% 4.50% 0.06% 0.02% NA
All Indica  2759 92.50% 7.30% 0.11% 0.04% NA
All Japonica  1512 99.80% 0.20% 0.00% 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 85.20% 14.40% 0.22% 0.22% NA
Indica III  913 91.00% 8.80% 0.22% 0.00% NA
Indica Intermediate  786 93.00% 7.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 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 91.10% 8.90% 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
vg0335957254 G -> A LOC_Os03g63650.1 downstream_gene_variant ; 2088.0bp to feature; MODIFIER silent_mutation Average:45.412; most accessible tissue: Callus, score: 84.982 N N N N
vg0335957254 G -> A LOC_Os03g63660.1 intron_variant ; MODIFIER silent_mutation Average:45.412; most accessible tissue: Callus, score: 84.982 N N N N
vg0335957254 G -> DEL N N silent_mutation Average:45.412; most accessible tissue: Callus, score: 84.982 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0335957254 NA 8.37E-07 mr1076 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
vg0335957254 NA 4.94E-06 mr1083 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
vg0335957254 NA 6.27E-08 mr1103 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
vg0335957254 NA 2.44E-07 mr1226 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
vg0335957254 NA 6.52E-08 mr1301 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
vg0335957254 NA 1.12E-07 mr1410 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
vg0335957254 NA 9.01E-06 mr1436 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
vg0335957254 NA 7.81E-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
vg0335957254 NA 1.09E-06 mr1560 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
vg0335957254 NA 1.22E-06 mr1949 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
vg0335957254 NA 6.91E-08 mr1949_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