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Detailed information for vg1128159591:

Variant ID: vg1128159591 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28159591
Reference Allele: T	Alternative Allele: C,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAGATATAATCCCTCCATCTATTATAGATATATTTTTAAATCTGAAAAATTTATTTTTAATAGACATATTTCAATTCAACAAACTATCATCTTAATGA[T/C,G]
TTTTTCGGATTTAATGCATGACTCTTTATTCTTCTACGCAAGATTGGCTATATGGGCATTGAGAAATGTAAATATTAATGAATCGTTTGTTTACGAGAAA

Reverse complement sequence

TTTCTCGTAAACAAACGATTCATTAATATTTACATTTCTCAATGCCCATATAGCCAATCTTGCGTAGAAGAATAAAGAGTCATGCATTAAATCCGAAAAA[A/G,C]
TCATTAAGATGATAGTTTGTTGAATTGAAATATGTCTATTAAAAATAAATTTTTCAGATTTAAAAATATATCTATAATAGATGGAGGGATTATATCTCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.10%	24.80%	1.29%	27.70%	G: 0.06%
All Indica	2759	61.20%	15.10%	0.94%	22.73%	G: 0.07%
All Japonica	1512	23.70%	39.20%	1.79%	35.38%	NA
Aus	269	29.00%	28.60%	1.12%	41.26%	NA
Indica I	595	55.00%	9.90%	1.34%	33.78%	NA
Indica II	465	83.20%	4.10%	0.00%	12.69%	NA
Indica III	913	57.30%	19.30%	0.88%	22.56%	NA
Indica Intermediate	786	57.40%	20.60%	1.27%	20.48%	G: 0.25%
Temperate Japonica	767	18.90%	31.70%	1.69%	47.72%	NA
Tropical Japonica	504	30.80%	51.40%	1.98%	15.87%	NA
Japonica Intermediate	241	24.10%	37.30%	1.66%	36.93%	NA
VI/Aromatic	96	24.00%	60.40%	1.04%	14.58%	NA
Intermediate	90	35.60%	34.40%	4.44%	24.44%	G: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128159591	T -> DEL	N	N	silent_mutation	Average:17.335; most accessible tissue: Callus, score: 36.675	N	N	N	N
vg1128159591	T -> G	LOC_Os11g46880.1	upstream_gene_variant ; 308.0bp to feature; MODIFIER	silent_mutation	Average:17.335; most accessible tissue: Callus, score: 36.675	N	N	N	N
vg1128159591	T -> G	LOC_Os11g46870-LOC_Os11g46880	intergenic_region ; MODIFIER	silent_mutation	Average:17.335; most accessible tissue: Callus, score: 36.675	N	N	N	N
vg1128159591	T -> C	LOC_Os11g46880.1	upstream_gene_variant ; 308.0bp to feature; MODIFIER	silent_mutation	Average:17.335; most accessible tissue: Callus, score: 36.675	N	N	N	N
vg1128159591	T -> C	LOC_Os11g46870-LOC_Os11g46880	intergenic_region ; MODIFIER	silent_mutation	Average:17.335; most accessible tissue: Callus, score: 36.675	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128159591	6.60E-06	NA	mr1520_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