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Detailed information for vg0612767306:

Variant ID: vg0612767306 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12767306
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTAGCGGGCCTACGGCTCCATCTTCACAGGTGCTCAACTGGGGTATAAGCCAGGGCTCCACCTAAGACTTCTTCTCTAAAGTTTCTCTTACTGAAGGG[A/G]
GGAAAGATAGAGCAACAATGAGTACAACCACAGTACTCAGCAAGCCACACCGGGAGATGCATGATTAATGCAAGGGGGTACAAGGGGTAATAATATAGGG

Reverse complement sequence

CCCTATATTATTACCCCTTGTACCCCCTTGCATTAATCATGCATCTCCCGGTGTGGCTTGCTGAGTACTGTGGTTGTACTCATTGTTGCTCTATCTTTCC[T/C]
CCCTTCAGTAAGAGAAACTTTAGAGAAGAAGTCTTAGGTGGAGCCCTGGCTTATACCCCAGTTGAGCACCTGTGAAGATGGAGCCGTAGGCCCGCTAGTC

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	66.90%	31.40%	1.67%	0.00%	NA
All Indica	2759	97.20%	2.20%	0.51%	0.00%	NA
All Japonica	1512	11.20%	88.50%	0.26%	0.00%	NA
Aus	269	65.40%	15.20%	19.33%	0.00%	NA
Indica I	595	96.50%	2.50%	1.01%	0.00%	NA
Indica II	465	97.20%	2.60%	0.22%	0.00%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	4.20%	0.76%	0.00%	NA
Temperate Japonica	767	3.10%	96.60%	0.26%	0.00%	NA
Tropical Japonica	504	24.00%	76.00%	0.00%	0.00%	NA
Japonica Intermediate	241	10.40%	88.80%	0.83%	0.00%	NA
VI/Aromatic	96	84.40%	13.50%	2.08%	0.00%	NA
Intermediate	90	58.90%	33.30%	7.78%	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
vg0612767306	A -> G	LOC_Os06g22030.1	upstream_gene_variant ; 3170.0bp to feature; MODIFIER	silent_mutation	Average:50.759; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N
vg0612767306	A -> G	LOC_Os06g22030-LOC_Os06g22040	intergenic_region ; MODIFIER	silent_mutation	Average:50.759; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612767306	3.12E-06	1.80E-07	mr1090	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
vg0612767306	3.14E-07	6.73E-08	mr1211	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
vg0612767306	NA	9.99E-08	mr1354	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