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Detailed information for vg0427271689:

Variant ID: vg0427271689 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27271689
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGTTGAACTCGAACAAACTCAGTGGTATAGAATAGATTTTCTCATTTTTTTTGGGGGAAAAAGAGAAACAAATCCCCTAAGAACATGTAGTTACGGTC[G/A]
TCATCGTCATCGCCGTCACTGAGTTGCGTTTGTCACCACGCCCAGGACCAACGACCGTCATCAACCCACCGGGGCCGCGCCACTCGGGTCAGCAACCCGC

Reverse complement sequence

GCGGGTTGCTGACCCGAGTGGCGCGGCCCCGGTGGGTTGATGACGGTCGTTGGTCCTGGGCGTGGTGACAAACGCAACTCAGTGACGGCGATGACGATGA[C/T]
GACCGTAACTACATGTTCTTAGGGGATTTGTTTCTCTTTTTCCCCCAAAAAAAATGAGAAAATCTATTCTATACCACTGAGTTTGTTCGAGTTCAACGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.90%	43.70%	0.13%	0.19%	NA
All Indica	2759	35.10%	64.40%	0.18%	0.33%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	8.90%	91.10%	0.00%	0.00%	NA
Indica I	595	21.50%	77.80%	0.17%	0.50%	NA
Indica II	465	10.50%	88.80%	0.22%	0.43%	NA
Indica III	913	51.00%	48.60%	0.11%	0.22%	NA
Indica Intermediate	786	41.50%	58.00%	0.25%	0.25%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg0427271689	G -> DEL	N	N	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46030.1	upstream_gene_variant ; 2709.0bp to feature; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46040.1	upstream_gene_variant ; 156.0bp to feature; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46050.1	downstream_gene_variant ; 3526.0bp to feature; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46050.2	downstream_gene_variant ; 3526.0bp to feature; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46050.3	downstream_gene_variant ; 3526.0bp to feature; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N
vg0427271689	G -> A	LOC_Os04g46030-LOC_Os04g46040	intergenic_region ; MODIFIER	silent_mutation	Average:53.851; most accessible tissue: Zhenshan97 young leaf, score: 66.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427271689	NA	9.62E-09	mr1212_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
vg0427271689	NA	7.22E-11	mr1216_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
vg0427271689	NA	8.16E-08	mr1408_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
vg0427271689	NA	4.03E-06	mr1536_2	Ind_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
vg0427271689	1.37E-06	1.37E-06	mr1574_2	Ind_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
vg0427271689	NA	1.52E-08	mr1600_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
vg0427271689	2.92E-06	2.92E-06	mr1781_2	Ind_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