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Detailed information for vg0221476316:

Variant ID: vg0221476316 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21476316
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ATCACATGGGCGTAAACTTGTCGGGATTTTACTGTTGCTCTTTATCTCGTGTTTGCTTTAAATTTGGGAGTGTTTTTTTAAGTTTACTTTGAAGTACACT[T/C]
GCTTCGAGTGATTTGGTGTAATAATCGGCTGTAGTTCGTTGAGTAATGACTGGGATGGTTTTCTATTCCATTATGTAAGAAAAACATAAGGTAGTAGTGA

Reverse complement sequence

TCACTACTACCTTATGTTTTTCTTACATAATGGAATAGAAAACCATCCCAGTCATTACTCAACGAACTACAGCCGATTATTACACCAAATCACTCGAAGC[A/G]
AGTGTACTTCAAAGTAAACTTAAAAAAACACTCCCAAATTTAAAGCAAACACGAGATAAAGAGCAACAGTAAAATCCCGACAAGTTTACGCCCATGTGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.30% 34.50% 0.06% 0.08% NA
All Indica  2759 98.20% 1.60% 0.07% 0.11% NA
All Japonica  1512 3.80% 96.10% 0.00% 0.07% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.30% 1.50% 0.17% 0.00% NA
Indica II  465 97.80% 1.90% 0.00% 0.22% NA
Indica III  913 98.50% 1.30% 0.11% 0.11% NA
Indica Intermediate  786 98.00% 1.90% 0.00% 0.13% NA
Temperate Japonica  767 1.40% 98.40% 0.00% 0.13% NA
Tropical Japonica  504 7.10% 92.90% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 1.11% 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
vg0221476316 T -> DEL N N silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N
vg0221476316 T -> C LOC_Os02g35750.1 downstream_gene_variant ; 2494.0bp to feature; MODIFIER silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N
vg0221476316 T -> C LOC_Os02g35750.2 downstream_gene_variant ; 848.0bp to feature; MODIFIER silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N
vg0221476316 T -> C LOC_Os02g35750.3 downstream_gene_variant ; 683.0bp to feature; MODIFIER silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N
vg0221476316 T -> C LOC_Os02g35760.1 intron_variant ; MODIFIER silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N
vg0221476316 T -> C LOC_Os02g35760.2 intron_variant ; MODIFIER silent_mutation Average:70.951; most accessible tissue: Callus, score: 81.857 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221476316 NA 1.04E-71 mr1014 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
vg0221476316 NA 1.99E-65 mr1027 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
vg0221476316 NA 4.10E-11 mr1128 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
vg0221476316 NA 5.55E-82 mr1134 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
vg0221476316 NA 3.34E-76 mr1135 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
vg0221476316 NA 1.72E-23 mr1375 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
vg0221476316 NA 7.86E-90 mr1504 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
vg0221476316 NA 7.36E-08 mr1514 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
vg0221476316 NA 1.10E-33 mr1670 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
vg0221476316 NA 2.53E-84 mr1672 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
vg0221476316 NA 7.16E-36 mr1682 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
vg0221476316 NA 7.88E-59 mr1695 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
vg0221476316 NA 1.11E-10 mr1714 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
vg0221476316 NA 2.46E-19 mr1754 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
vg0221476316 NA 4.00E-18 mr1767 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
vg0221476316 3.32E-06 3.32E-06 mr1918 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
vg0221476316 NA 2.34E-100 mr1987 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
vg0221476316 NA 2.44E-12 mr1128_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
vg0221476316 NA 2.90E-17 mr1416_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
vg0221476316 NA 1.59E-06 mr1911_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