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Detailed information for vg0727965800:

Variant ID: vg0727965800 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27965800
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CCCGCTTCAACCAGGAGGATACTTCAAGTTTTAACGATCTAGATGAACATAGGTAATATTGATTTTATTTAACTCCAATTGTTTCCTTCTCTATGTTCAG[G/A]
TCGGACAAGACCTTGATCTGCACTTTTGCGTTTTACTCTGTAAATTTACTTCAAGCTAGTTAATGCTGATGAAGTATTTACTTTTTAGTCCAACAGGTTA

Reverse complement sequence

TAACCTGTTGGACTAAAAAGTAAATACTTCATCAGCATTAACTAGCTTGAAGTAAATTTACAGAGTAAAACGCAAAAGTGCAGATCAAGGTCTTGTCCGA[C/T]
CTGAACATAGAGAAGGAAACAATTGGAGTTAAATAAAATCAATATTACCTATGTTCATCTAGATCGTTAAAACTTGAAGTATCCTCCTGGTTGAAGCGGG

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 99.20% 0.50% 0.28% 0.00% NA
All Indica  2759 99.60% 0.30% 0.14% 0.00% NA
All Japonica  1512 98.30% 1.10% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.40% 0.38% 0.00% NA
Temperate Japonica  767 96.60% 2.20% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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  90 100.00% 0.00% 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
vg0727965800 G -> A LOC_Os07g46800.1 downstream_gene_variant ; 3890.0bp to feature; MODIFIER silent_mutation Average:51.275; most accessible tissue: Callus, score: 75.091 N N N N
vg0727965800 G -> A LOC_Os07g46790.1 intron_variant ; MODIFIER silent_mutation Average:51.275; most accessible tissue: Callus, score: 75.091 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727965800 6.22E-07 4.59E-07 mr1940 Jap_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
vg0727965800 NA 7.65E-06 mr1735_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