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Detailed information for vg1121621866:

Variant ID: vg1121621866 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21621866
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GGACCCCCGGCATGTCGGACGGCTGCCAAGCGAACACGTCAGCATTATCACGGAGGAAGGTGATGAGCGCGAGTTCCTATTTCTCGTTTAGTGTCGCCCC[A/G]
ATCTTGACGGTCTTGTCGGGGTTGGCACTGGAGAGTGGAACGATCTTGATGGTGCCGTCCGGTTTCGGCGTCTTGTTTGTCTTGCTCACTTTCTTGGGTG

Reverse complement sequence

CACCCAAGAAAGTGAGCAAGACAAACAAGACGCCGAAACCGGACGGCACCATCAAGATCGTTCCACTCTCCAGTGCCAACCCCGACAAGACCGTCAAGAT[T/C]
GGGGCGACACTAAACGAGAAATAGGAACTCGCGCTCATCACCTTCCTCCGTGATAATGCTGACGTGTTCGCTTGGCAGCCGTCCGACATGCCGGGGGTCC

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	33.90%	33.00%	25.03%	8.10%	NA
All Indica	2759	47.40%	13.10%	37.37%	2.10%	NA
All Japonica	1512	1.10%	73.50%	5.29%	20.11%	NA
Aus	269	66.20%	13.40%	16.73%	3.72%	NA
Indica I	595	27.70%	21.80%	46.55%	3.87%	NA
Indica II	465	35.30%	14.20%	49.46%	1.08%	NA
Indica III	913	69.80%	3.80%	25.63%	0.77%	NA
Indica Intermediate	786	43.50%	16.70%	36.90%	2.93%	NA
Temperate Japonica	767	0.70%	83.60%	6.13%	9.65%	NA
Tropical Japonica	504	1.40%	59.30%	5.56%	33.73%	NA
Japonica Intermediate	241	2.10%	71.00%	2.07%	24.90%	NA
VI/Aromatic	96	75.00%	17.70%	5.21%	2.08%	NA
Intermediate	90	27.80%	37.80%	24.44%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121621866	A -> DEL	N	N	silent_mutation	Average:16.372; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1121621866	A -> G	LOC_Os11g36630.1	downstream_gene_variant ; 3830.0bp to feature; MODIFIER	silent_mutation	Average:16.372; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1121621866	A -> G	LOC_Os11g36640.1	intron_variant ; MODIFIER	silent_mutation	Average:16.372; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121621866	8.09E-06	NA	mr1128	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