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Detailed information for vg1116501862:

Variant ID: vg1116501862 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16501862
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CCGATCAATATATTTCTTCCGTATATCTAGACTTCTCATATGCGGTTAATATGTTTGGTACGTTTAGTTTTGCATATATACTAGCTACCTAGGTATTCAT[C/G]
AAAACCATCGATCGTCGCGTCGATAGGCGTACGTGGAGTCGATCCGGTGGAATTCGTCAAAACCGTGGATGCATGCATGCATGCATACGTGTTTCTTGCG

Reverse complement sequence

CGCAAGAAACACGTATGCATGCATGCATGCATCCACGGTTTTGACGAATTCCACCGGATCGACTCCACGTACGCCTATCGACGCGACGATCGATGGTTTT[G/C]
ATGAATACCTAGGTAGCTAGTATATATGCAAAACTAAACGTACCAAACATATTAACCGCATATGAGAAGTCTAGATATACGGAAGAAATATATTGATCGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.90%	14.50%	0.83%	29.75%	NA
All Indica	2759	29.30%	21.00%	1.27%	48.39%	NA
All Japonica	1512	94.80%	4.00%	0.13%	1.06%	NA
Aus	269	77.30%	12.60%	0.00%	10.04%	NA
Indica I	595	18.20%	10.30%	1.85%	69.75%	NA
Indica II	465	48.20%	7.50%	1.72%	42.58%	NA
Indica III	913	20.80%	37.60%	0.66%	40.96%	NA
Indica Intermediate	786	36.50%	17.90%	1.27%	44.27%	NA
Temperate Japonica	767	97.40%	1.40%	0.13%	1.04%	NA
Tropical Japonica	504	89.90%	8.70%	0.20%	1.19%	NA
Japonica Intermediate	241	96.70%	2.50%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	2.10%	0.00%	2.08%	NA
Intermediate	90	57.80%	11.10%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116501862	C -> DEL	N	N	silent_mutation	Average:26.445; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N
vg1116501862	C -> G	LOC_Os11g28590-LOC_Os11g28600	intergenic_region ; MODIFIER	silent_mutation	Average:26.445; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116501862	NA	3.84E-06	mr1502	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
vg1116501862	8.85E-07	2.51E-08	mr1502	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