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Detailed information for vg0304861604:

Variant ID: vg0304861604 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4861604
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.13, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGATTTTGAGTTTTTACATGTAACGTTTGACCACTCGTCTTATTCAAATTTTTTTGAAATTATTATTTATTTTATTTGTGACTTACTATTATCTACA[G/A]
TACTTTAAACACAACTTTTTATTTTTTATATTTGCAAAAAAAAACTGAATAAGACGAGTGGTCAAACGTTACAATCAAAAACTCAAAATCCCTTATATTG

Reverse complement sequence

CAATATAAGGGATTTTGAGTTTTTGATTGTAACGTTTGACCACTCGTCTTATTCAGTTTTTTTTTGCAAATATAAAAAATAAAAAGTTGTGTTTAAAGTA[C/T]
TGTAGATAATAGTAAGTCACAAATAAAATAAATAATAATTTCAAAAAAATTTGAATAAGACGAGTGGTCAAACGTTACATGTAAAAACTCAAAATCCCTT

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 34.30% 9.90% 16.55% 39.25% NA
All Indica  2759 2.40% 15.40% 27.00% 55.20% NA
All Japonica  1512 96.80% 2.10% 0.66% 0.46% NA
Aus  269 0.70% 1.90% 0.74% 96.65% NA
Indica I  595 0.80% 13.90% 40.84% 44.37% NA
Indica II  465 8.40% 13.50% 29.25% 48.82% NA
Indica III  913 0.30% 16.80% 18.18% 64.73% NA
Indica Intermediate  786 2.40% 16.00% 25.45% 56.11% NA
Temperate Japonica  767 94.10% 3.90% 1.30% 0.65% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 38.50% 2.10% 11.46% 47.92% NA
Intermediate  90 55.60% 7.80% 15.56% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0304861604 G -> A LOC_Os03g09290.1 downstream_gene_variant ; 4070.0bp to feature; MODIFIER silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0304861604 G -> A LOC_Os03g09300.1 downstream_gene_variant ; 1231.0bp to feature; MODIFIER silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0304861604 G -> A LOC_Os03g09310.1 downstream_gene_variant ; 579.0bp to feature; MODIFIER silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0304861604 G -> A LOC_Os03g09310.2 downstream_gene_variant ; 580.0bp to feature; MODIFIER silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0304861604 G -> A LOC_Os03g09300-LOC_Os03g09310 intergenic_region ; MODIFIER silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0304861604 G -> DEL N N silent_mutation Average:20.504; most accessible tissue: Minghui63 root, score: 33.152 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304861604 NA 9.45E-16 mr1062 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
vg0304861604 NA 5.46E-06 mr1062 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
vg0304861604 NA 1.44E-15 mr1146 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
vg0304861604 2.82E-09 NA mr1210 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
vg0304861604 2.23E-08 1.41E-10 mr1210 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
vg0304861604 1.91E-07 NA mr1305 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
vg0304861604 3.53E-06 5.50E-08 mr1305 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
vg0304861604 NA 9.89E-07 mr1358 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
vg0304861604 NA 6.99E-06 mr1515 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
vg0304861604 NA 3.42E-18 mr1529 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
vg0304861604 8.71E-08 NA mr1585 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
vg0304861604 4.52E-07 3.23E-11 mr1585 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
vg0304861604 8.00E-10 NA mr1586 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
vg0304861604 2.74E-07 1.01E-09 mr1586 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
vg0304861604 NA 7.14E-11 mr1623 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
vg0304861604 NA 6.24E-61 mr1711 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
vg0304861604 NA 1.98E-88 mr1758 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
vg0304861604 NA 2.03E-06 mr1765 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
vg0304861604 3.91E-07 NA mr1305_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
vg0304861604 3.82E-06 1.54E-08 mr1305_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
vg0304861604 NA 7.54E-06 mr1559_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
vg0304861604 5.80E-07 NA mr1585_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
vg0304861604 NA 1.55E-09 mr1585_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
vg0304861604 NA 9.41E-30 mr1631_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
vg0304861604 NA 4.41E-08 mr1693_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
vg0304861604 NA 4.54E-13 mr1717_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
vg0304861604 NA 2.27E-08 mr1765_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
vg0304861604 NA 3.10E-20 mr1900_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