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Detailed information for vg1114991627:

Variant ID: vg1114991627 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14991627
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TAAACCAACATCTAGTCATTTTGATACCCAAGTTATCAATGGCATAAGGTAAACAATATATGGCTGAGTAATAGGACCCATCCCACATGACATTGTAAAA[G/T]
AATGCAACATTTAATAGAAATGCGGCATATTTGTAAATTGGGTATAATATGATCAATTGTAATGCATGACTTGCCTTGCTCTCGCACTGATGAGACTTCA

Reverse complement sequence

TGAAGTCTCATCAGTGCGAGAGCAAGGCAAGTCATGCATTACAATTGATCATATTATACCCAATTTACAAATATGCCGCATTTCTATTAAATGTTGCATT[C/A]
TTTTACAATGTCATGTGGGATGGGTCCTATTACTCAGCCATATATTGTTTACCTTATGCCATTGATAACTTGGGTATCAAAATGACTAGATGTTGGTTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	6.80%	0.44%	0.00%	NA
All Indica	2759	98.80%	0.60%	0.54%	0.00%	NA
All Japonica	1512	79.90%	19.90%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	1.30%	1.78%	0.00%	NA
Temperate Japonica	767	66.10%	33.60%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	17.40%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	2.10%	3.12%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg1114991627	G -> T	LOC_Os11g26180.1	upstream_gene_variant ; 269.0bp to feature; MODIFIER	silent_mutation	Average:40.979; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1114991627	G -> T	LOC_Os11g26180-LOC_Os11g26190	intergenic_region ; MODIFIER	silent_mutation	Average:40.979; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114991627	NA	6.74E-06	mr1424	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
vg1114991627	4.62E-06	NA	mr1604	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