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Detailed information for vg1125137642:

Variant ID: vg1125137642 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25137642
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAAACCACCTATACTTGTGTAATTAAAGCGGTGATATCTTCATTTTTTAAAAAAAAAATAAGCATTAACATCAAACAGGGGCGGAGCTAGAACGAAAT[G/A]
GAGGGGTGCTTAATTTACTTTATTTTATATAGAGTTTAAGTTGATACGGTGATCTAAATTTGTGTTGAGAGTGGTGCATACATGGTGAAAACAGTGAGTT

Reverse complement sequence

AACTCACTGTTTTCACCATGTATGCACCACTCTCAACACAAATTTAGATCACCGTATCAACTTAAACTCTATATAAAATAAAGTAAATTAAGCACCCCTC[C/T]
ATTTCGTTCTAGCTCCGCCCCTGTTTGATGTTAATGCTTATTTTTTTTTTAAAAAATGAAGATATCACCGCTTTAATTACACAAGTATAGGTGGTTTCCT

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	48.20%	44.80%	0.68%	6.28%	NA
All Indica	2759	31.10%	59.80%	0.76%	8.34%	NA
All Japonica	1512	81.70%	16.90%	0.60%	0.73%	NA
Aus	269	24.90%	55.80%	0.74%	18.59%	NA
Indica I	595	64.20%	33.30%	0.50%	2.02%	NA
Indica II	465	25.20%	72.70%	0.00%	2.15%	NA
Indica III	913	20.80%	65.60%	1.42%	12.16%	NA
Indica Intermediate	786	21.50%	65.50%	0.64%	12.34%	NA
Temperate Japonica	767	93.90%	5.10%	0.00%	1.04%	NA
Tropical Japonica	504	72.60%	26.80%	0.60%	0.00%	NA
Japonica Intermediate	241	62.20%	34.00%	2.49%	1.24%	NA
VI/Aromatic	96	70.80%	28.10%	0.00%	1.04%	NA
Intermediate	90	55.60%	38.90%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125137642	G -> A	LOC_Os11g41800-LOC_Os11g41820	intergenic_region ; MODIFIER	silent_mutation	Average:36.972; most accessible tissue: Zhenshan97 young leaf, score: 54.618	N	N	N	N
vg1125137642	G -> DEL	N	N	silent_mutation	Average:36.972; most accessible tissue: Zhenshan97 young leaf, score: 54.618	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125137642	NA	4.60E-07	mr1191_2	Ind_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
vg1125137642	NA	4.05E-06	mr1531_2	Jap_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
vg1125137642	NA	1.52E-06	mr1609_2	Ind_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
vg1125137642	NA	8.17E-06	mr1745_2	Ind_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
vg1125137642	NA	1.72E-06	mr1788_2	Jap_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
vg1125137642	9.98E-06	9.83E-07	mr1793_2	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