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Detailed information for vg1105850609:

Variant ID: vg1105850609 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5850609
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.41, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

GCCCTATATTAAGAAGAATGGGCCTAGTCTACGAGGGAGACCAAACCCAAAAACCATACAACCAAACAATAAATTAAGAAAACCATCAAAACCTACACAA[A/G]
GGGCAAAAGAGAAACAACCTGTGGCGATAGGACTACTAAGGCACGACTGAAGACATCGAGCAACTCCGACTTCCTAAGACAAGCCAGAACATACCAACAA

Reverse complement sequence

TTGTTGGTATGTTCTGGCTTGTCTTAGGAAGTCGGAGTTGCTCGATGTCTTCAGTCGTGCCTTAGTAGTCCTATCGCCACAGGTTGTTTCTCTTTTGCCC[T/C]
TTGTGTAGGTTTTGATGGTTTTCTTAATTTATTGTTTGGTTGTATGGTTTTTGGGTTTGGTCTCCCTCGTAGACTAGGCCCATTCTTCTTAATATAGGGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.70%	9.70%	0.99%	43.67%	NA
All Indica	2759	17.90%	10.70%	1.56%	69.81%	NA
All Japonica	1512	92.50%	2.20%	0.20%	5.09%	NA
Aus	269	48.30%	42.80%	0.37%	8.55%	NA
Indica I	595	6.90%	9.10%	1.01%	83.03%	NA
Indica II	465	8.00%	5.40%	2.80%	83.87%	NA
Indica III	913	26.20%	11.20%	1.20%	61.45%	NA
Indica Intermediate	786	22.50%	14.60%	1.65%	61.20%	NA
Temperate Japonica	767	91.90%	1.30%	0.39%	6.39%	NA
Tropical Japonica	504	97.40%	1.00%	0.00%	1.59%	NA
Japonica Intermediate	241	83.80%	7.90%	0.00%	8.30%	NA
VI/Aromatic	96	91.70%	5.20%	0.00%	3.12%	NA
Intermediate	90	53.30%	7.80%	0.00%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105850609	A -> DEL	N	N	silent_mutation	Average:14.163; most accessible tissue: Callus, score: 60.194	N	N	N	N
vg1105850609	A -> G	LOC_Os11g10670.1	downstream_gene_variant ; 1444.0bp to feature; MODIFIER	silent_mutation	Average:14.163; most accessible tissue: Callus, score: 60.194	N	N	N	N
vg1105850609	A -> G	LOC_Os11g10650-LOC_Os11g10670	intergenic_region ; MODIFIER	silent_mutation	Average:14.163; most accessible tissue: Callus, score: 60.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105850609	1.05E-06	3.98E-07	mr1312_2	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
vg1105850609	9.50E-06	9.48E-06	mr1412_2	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
vg1105850609	4.65E-06	7.98E-07	mr1663_2	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
vg1105850609	7.66E-06	5.88E-06	mr1832_2	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