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Detailed information for vg1107481747:

Variant ID: vg1107481747 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7481747
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTACATAATAATAAGCAACTATCTATATGTCCTATCTAGCAATCATTTTTTTAAATGACTTTATCAATACTTAAAGACTTATATGTTAATCTTCTACAAT[A/G]
ATTAATTAGGCTTGCTAATGCATTAAATACATATGGATTTAATAGACTGGACTTCATTATGGATTAGCTTTGGGTGGATAGAAATTAGTTAATGCAGCTA

Reverse complement sequence

TAGCTGCATTAACTAATTTCTATCCACCCAAAGCTAATCCATAATGAAGTCCAGTCTATTAAATCCATATGTATTTAATGCATTAGCAAGCCTAATTAAT[T/C]
ATTGTAGAAGATTAACATATAAGTCTTTAAGTATTGATAAAGTCATTTAAAAAAATGATTGCTAGATAGGACATATAGATAGTTGCTTATTATTATGTAC

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	87.80%	12.10%	0.04%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	68.60%	31.30%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.40%	0.00%	0.00%	NA
Temperate Japonica	767	67.70%	32.30%	0.00%	0.00%	NA
Tropical Japonica	504	74.40%	25.40%	0.20%	0.00%	NA
Japonica Intermediate	241	59.30%	40.70%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	78.90%	20.00%	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
vg1107481747	A -> G	LOC_Os11g13650-LOC_Os11g13660	intergenic_region ; MODIFIER	silent_mutation	Average:27.831; most accessible tissue: Callus, score: 64.564	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107481747	3.72E-06	NA	mr1961	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
vg1107481747	NA	4.30E-07	mr1961	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