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Detailed information for vg1107898019:

Variant ID: vg1107898019 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7898019
Reference Allele: A	Alternative Allele: G
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCTTATGAGTAATACGATCACGAATAATAGCATTTCTTTGTATCACTTCTTCCATCTCTGGGTTAGGTCCTTGTGAGATTGTAGCTTCTTATACAGTT[A/G]
ATGTGCTTGGTGTCTCATTCAAATCAAGAGGAAGCTGCTCGATGTCTTTCTCATCTTCGATTACCATGTTGTGAAGGATAATACAAGCTAGCATGATATT

Reverse complement sequence

AATATCATGCTAGCTTGTATTATCCTTCACAACATGGTAATCGAAGATGAGAAAGACATCGAGCAGCTTCCTCTTGATTTGAATGAGACACCAAGCACAT[T/C]
AACTGTATAAGAAGCTACAATCTCACAAGGACCTAACCCAGAGATGGAAGAAGTGATACAAAGAAATGCTATTATTCGTGATCGTATTACTCATAAGCAA

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	65.60%	34.40%	0.04%	0.00%	NA
All Indica	2759	96.30%	3.70%	0.00%	0.00%	NA
All Japonica	1512	12.40%	87.50%	0.07%	0.00%	NA
Aus	269	48.70%	51.30%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	96.50%	3.50%	0.00%	0.00%	NA
Indica Intermediate	786	92.70%	7.30%	0.00%	0.00%	NA
Temperate Japonica	767	4.20%	95.80%	0.00%	0.00%	NA
Tropical Japonica	504	24.20%	75.60%	0.20%	0.00%	NA
Japonica Intermediate	241	14.10%	85.90%	0.00%	0.00%	NA
VI/Aromatic	96	65.60%	34.40%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	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
vg1107898019	A -> G	LOC_Os11g14160.1	downstream_gene_variant ; 1815.0bp to feature; MODIFIER	silent_mutation	Average:42.456; most accessible tissue: Zhenshan97 flower, score: 60.301	N	N	N	N
vg1107898019	A -> G	LOC_Os11g14150.1	intron_variant ; MODIFIER	silent_mutation	Average:42.456; most accessible tissue: Zhenshan97 flower, score: 60.301	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107898019	3.92E-08	3.92E-08	mr1761	Jap_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