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Detailed information for vg1117979612:

Variant ID: vg1117979612 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17979612
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATTTATCATTAAACAAACTATTATAATATGTAACTCTTTTTATTTAAAACATCTTAGTTTTATAGATATTGTTGGTCAAAGTAGCATCTCGGAGATT[G/A]
TGTCAGAGTCAAAAATGTTTATATTTTAGGATAGAGGGAGTAGCTTTTTTTATGAAAAATGGATTAACAAGATTTTTGAAATAAAATTTGCAAATTTGCC

Reverse complement sequence

GGCAAATTTGCAAATTTTATTTCAAAAATCTTGTTAATCCATTTTTCATAAAAAAAGCTACTCCCTCTATCCTAAAATATAAACATTTTTGACTCTGACA[C/T]
AATCTCCGAGATGCTACTTTGACCAACAATATCTATAAAACTAAGATGTTTTAAATAAAAAGAGTTACATATTATAATAGTTTGTTTAATGATAAATCTA

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	61.70%	31.60%	0.21%	6.45%	NA
All Indica	2759	40.20%	52.50%	0.11%	7.21%	NA
All Japonica	1512	95.80%	0.90%	0.00%	3.24%	NA
Aus	269	89.60%	0.00%	0.37%	10.04%	NA
Indica I	595	27.70%	63.90%	0.34%	8.07%	NA
Indica II	465	40.60%	58.30%	0.00%	1.08%	NA
Indica III	913	45.20%	44.70%	0.00%	10.08%	NA
Indica Intermediate	786	43.40%	49.60%	0.13%	6.87%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	91.50%	0.40%	0.00%	8.13%	NA
Japonica Intermediate	241	94.60%	2.10%	0.00%	3.32%	NA
VI/Aromatic	96	70.80%	1.00%	3.12%	25.00%	NA
Intermediate	90	56.70%	33.30%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117979612	G -> A	LOC_Os11g30880-LOC_Os11g30910	intergenic_region ; MODIFIER	silent_mutation	Average:21.95; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1117979612	G -> DEL	N	N	silent_mutation	Average:21.95; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117979612	7.03E-08	5.44E-07	mr1800	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
vg1117979612	4.47E-07	3.86E-08	mr1800	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