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Detailed information for vg0629542107:

Variant ID: vg0629542107 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29542107
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTTTGCTATCACAGAGCCAATGATGAAAGGAAGGTTCATTGATCGGCAAGCATTTCGAAAGCCCAATTGCTCTGAGAGCAATCCACCACAGCTGCC[A/G]
AGACTCTGGACATGCAACCAAAAGGTGATCGATAGTCTCGTCACTTTGATCACAAAGAACGCAACGCACAGGGTGCGACAAGCCATGGCTCTGGAGACGG

Reverse complement sequence

CCGTCTCCAGAGCCATGGCTTGTCGCACCCTGTGCGTTGCGTTCTTTGTGATCAAAGTGACGAGACTATCGATCACCTTTTGGTTGCATGTCCAGAGTCT[T/C]
GGCAGCTGTGGTGGATTGCTCTCAGAGCAATTGGGCTTTCGAAATGCTTGCCGATCAATGAACCTTCCTTTCATCATTGGCTCTGTGATAGCAAAAAGAA

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	70.10%	27.00%	0.02%	2.88%	NA
All Indica	2759	94.10%	4.50%	0.00%	1.41%	NA
All Japonica	1512	26.70%	73.30%	0.00%	0.07%	NA
Aus	269	62.50%	2.60%	0.00%	34.94%	NA
Indica I	595	89.60%	10.40%	0.00%	0.00%	NA
Indica II	465	95.30%	1.50%	0.00%	3.23%	NA
Indica III	913	98.80%	0.70%	0.00%	0.55%	NA
Indica Intermediate	786	91.20%	6.40%	0.00%	2.42%	NA
Temperate Japonica	767	20.70%	79.30%	0.00%	0.00%	NA
Tropical Japonica	504	30.00%	70.00%	0.00%	0.00%	NA
Japonica Intermediate	241	38.60%	61.00%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	64.40%	32.20%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0629542107	A -> G	LOC_Os06g48810.1	upstream_gene_variant ; 888.0bp to feature; MODIFIER	silent_mutation	Average:65.41; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0629542107	A -> G	LOC_Os06g48810-LOC_Os06g48820	intergenic_region ; MODIFIER	silent_mutation	Average:65.41; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N
vg0629542107	A -> DEL	N	N	silent_mutation	Average:65.41; most accessible tissue: Zhenshan97 young leaf, score: 81.6	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629542107	3.96E-06	6.73E-07	mr1851	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
vg0629542107	NA	1.39E-17	mr1968	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
vg0629542107	NA	2.68E-21	mr1968_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