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Detailed information for vg0818051791:

Variant ID: vg0818051791 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18051791
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATTCTCATTTTCCTGAGTTACTATAAACATCCATTTCACAGTGGTACACCTCTGGCTAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGG[T/C]
GGGTCTAACAATGTCTTTCGTGATTAGTCTCACACTTCTCACCATAATAAAAGATGCTATAACTGGTAATAATTTGATTAGCTCCTGGTTTGGAATGGTA

Reverse complement sequence

TACCATTCCAAACCAGGAGCTAATCAAATTATTACCAGTTATAGCATCTTTTATTATGGTGAGAAGTGTGAGACTAATCACGAAAGACATTGTTAGACCC[A/G]
CCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACTCTAGCCAGAGGTGTACCACTGTGAAATGGATGTTTATAGTAACTCAGGAAAATGAGAATAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.20%	21.90%	0.74%	15.13%	NA
All Indica	2759	89.00%	2.30%	0.83%	7.87%	NA
All Japonica	1512	22.90%	62.20%	0.20%	14.68%	NA
Aus	269	2.60%	3.00%	2.60%	91.82%	NA
Indica I	595	89.10%	5.70%	0.84%	4.37%	NA
Indica II	465	91.60%	1.10%	1.94%	5.38%	NA
Indica III	913	91.30%	0.40%	0.55%	7.67%	NA
Indica Intermediate	786	84.60%	2.70%	0.51%	12.21%	NA
Temperate Japonica	767	13.20%	85.30%	0.00%	1.56%	NA
Tropical Japonica	504	30.00%	32.10%	0.40%	37.50%	NA
Japonica Intermediate	241	39.00%	51.90%	0.41%	8.71%	NA
VI/Aromatic	96	86.50%	1.00%	0.00%	12.50%	NA
Intermediate	90	54.40%	24.40%	2.22%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818051791	T -> C	LOC_Os08g29440.1	downstream_gene_variant ; 1812.0bp to feature; MODIFIER	silent_mutation	Average:47.142; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N
vg0818051791	T -> C	LOC_Os08g29450.1	downstream_gene_variant ; 2742.0bp to feature; MODIFIER	silent_mutation	Average:47.142; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N
vg0818051791	T -> C	LOC_Os08g29440-LOC_Os08g29450	intergenic_region ; MODIFIER	silent_mutation	Average:47.142; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N
vg0818051791	T -> DEL	N	N	silent_mutation	Average:47.142; most accessible tissue: Minghui63 young leaf, score: 75.937	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818051791	NA	4.27E-06	mr1182	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
vg0818051791	3.37E-06	NA	mr1907	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