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Detailed information for vg0330806269:

Variant ID: vg0330806269 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30806269
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TATATGGTATTGGAACATATCATTGACTACATGAATGCATGATGCCAATTGCTTTTTTTTGTCAAGTTGCATTATAAGCTCAAACCTTTTATTCAGTTGT[C/T]
CTAGTTGATTGACCACTTCATATTTGTGGGAAATCAACTGCTGAATTTATTCAAACTTTTCATTTAGCAATATTACTAATTGAAAAGTTCTCTGAGTAAT

Reverse complement sequence

ATTACTCAGAGAACTTTTCAATTAGTAATATTGCTAAATGAAAAGTTTGAATAAATTCAGCAGTTGATTTCCCACAAATATGAAGTGGTCAATCAACTAG[G/A]
ACAACTGAATAAAAGGTTTGAGCTTATAATGCAACTTGACAAAAAAAAGCAATTGGCATCATGCATTCATGTAGTCAATGATATGTTCCAATACCATATA

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 94.00% 5.60% 0.40% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 82.00% 16.70% 1.26% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 47.80% 48.60% 3.57% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0330806269 C -> T LOC_Os03g53720.2 3_prime_UTR_variant ; 1228.0bp to feature; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N
vg0330806269 C -> T LOC_Os03g53740.1 upstream_gene_variant ; 2760.0bp to feature; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N
vg0330806269 C -> T LOC_Os03g53730.1 downstream_gene_variant ; 1379.0bp to feature; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N
vg0330806269 C -> T LOC_Os03g53750.1 downstream_gene_variant ; 3996.0bp to feature; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N
vg0330806269 C -> T LOC_Os03g53750.2 downstream_gene_variant ; 3996.0bp to feature; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N
vg0330806269 C -> T LOC_Os03g53720.1 intron_variant ; MODIFIER silent_mutation Average:45.382; most accessible tissue: Callus, score: 85.483 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330806269 2.40E-07 NA mr1019 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
vg0330806269 5.35E-06 NA mr1019 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
vg0330806269 NA 2.31E-06 mr1248 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
vg0330806269 3.51E-06 NA 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
vg0330806269 NA 1.16E-06 mr1742 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