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Detailed information for vg1105881057:

Variant ID: vg1105881057 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5881057
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.03, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCGTTCTATAAGAAAGACTGGAGTTAATAGTAGCACTTTAAATCTTAACTGAAATTTCTCAAATCCTGGATTAGGGTATAGACTAAATGTGAATGAAA[T/A]
TAATACAGAGAGAAAGTTCAAAACAAGCCCTCAGATGTGCATCATTTGGAGAAAAATTGAATGAGTTTTTACCTAGTTTTGTTACCCCAACAACTTTCAT

Reverse complement sequence

ATGAAAGTTGTTGGGGTAACAAAACTAGGTAAAAACTCATTCAATTTTTCTCCAAATGATGCACATCTGAGGGCTTGTTTTGAACTTTCTCTCTGTATTA[A/T]
TTTCATTCACATTTAGTCTATACCCTAATCCAGGATTTGAGAAATTTCAGTTAAGATTTAAAGTGCTACTATTAACTCCAGTCTTTCTTATAGAACGAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.00%	29.30%	0.08%	0.63%	NA
All Indica	2759	98.50%	1.40%	0.04%	0.04%	NA
All Japonica	1512	16.60%	83.30%	0.07%	0.00%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	97.20%	2.70%	0.00%	0.13%	NA
Temperate Japonica	767	6.80%	93.20%	0.00%	0.00%	NA
Tropical Japonica	504	31.70%	68.10%	0.20%	0.00%	NA
Japonica Intermediate	241	16.20%	83.80%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	55.20%	0.00%	28.12%	NA
Intermediate	90	68.90%	26.70%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105881057	T -> A	LOC_Os11g10710.1	upstream_gene_variant ; 344.0bp to feature; MODIFIER	silent_mutation	Average:45.9; most accessible tissue: Callus, score: 83.836	N	N	N	N
vg1105881057	T -> A	LOC_Os11g10710-LOC_Os11g10720	intergenic_region ; MODIFIER	silent_mutation	Average:45.9; most accessible tissue: Callus, score: 83.836	N	N	N	N
vg1105881057	T -> DEL	N	N	silent_mutation	Average:45.9; most accessible tissue: Callus, score: 83.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105881057	7.56E-06	2.78E-06	mr1662_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
vg1105881057	1.57E-06	NA	mr1870_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