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Detailed information for vg0630043980:

Variant ID: vg0630043980 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30043980
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.11, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAATCACCAGTGTAACACCCTGAAAATTCGACCAACGAAATCAAAACACCAAAAATATTGCATCATGCCGATTTTATTCGCCTATTTCATTAGATTTT[A/G]
ATCTCGGAATTTATTAATCGCGAATAATGAATAACTAACTAGGAATAAACCCTAAAAATCAAGTTGGCTAAATAAATAATTAAAATATAAATTAAAATAA

Reverse complement sequence

TTATTTTAATTTATATTTTAATTATTTATTTAGCCAACTTGATTTTTAGGGTTTATTCCTAGTTAGTTATTCATTATTCGCGATTAATAAATTCCGAGAT[T/C]
AAAATCTAATGAAATAGGCGAATAAAATCGGCATGATGCAATATTTTTGGTGTTTTGATTTCGTTGGTCGAATTTTCAGGGTGTTACACTGGTGATTCAT

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 68.60% 16.40% 12.61% 2.45% NA
All Indica  2759 93.80% 0.40% 2.65% 3.19% NA
All Japonica  1512 19.30% 50.00% 29.10% 1.59% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.60% 0.30% 1.01% 9.08% NA
Indica II  465 99.10% 0.20% 0.65% 0.00% NA
Indica III  913 95.10% 0.10% 4.38% 0.44% NA
Indica Intermediate  786 92.20% 0.90% 3.05% 3.82% NA
Temperate Japonica  767 6.30% 90.00% 3.65% 0.13% NA
Tropical Japonica  504 39.50% 2.20% 55.95% 2.38% NA
Japonica Intermediate  241 18.70% 22.80% 53.94% 4.56% NA
VI/Aromatic  96 24.00% 0.00% 73.96% 2.08% NA
Intermediate  90 76.70% 7.80% 13.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630043980 A -> G LOC_Os06g49650.1 upstream_gene_variant ; 4404.0bp to feature; MODIFIER silent_mutation Average:20.181; most accessible tissue: Callus, score: 44.454 N N N N
vg0630043980 A -> G LOC_Os06g49650-LOC_Os06g49660 intergenic_region ; MODIFIER silent_mutation Average:20.181; most accessible tissue: Callus, score: 44.454 N N N N
vg0630043980 A -> DEL N N silent_mutation Average:20.181; most accessible tissue: Callus, score: 44.454 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630043980 NA 1.59E-67 mr1489 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
vg0630043980 NA 5.19E-08 mr1543 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
vg0630043980 NA 3.16E-07 mr1584 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
vg0630043980 NA 1.59E-08 mr1593 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
vg0630043980 NA 5.15E-14 mr1653 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
vg0630043980 NA 9.62E-07 mr1815 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
vg0630043980 NA 8.76E-09 mr1866 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
vg0630043980 2.76E-08 NA mr1871 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
vg0630043980 NA 1.43E-08 mr1871 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
vg0630043980 NA 6.44E-07 mr1347_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
vg0630043980 NA 1.77E-07 mr1350_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
vg0630043980 NA 5.70E-11 mr1368_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
vg0630043980 NA 1.01E-09 mr1543_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
vg0630043980 NA 6.75E-07 mr1582_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
vg0630043980 NA 1.60E-09 mr1584_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
vg0630043980 NA 4.37E-09 mr1871_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