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Detailed information for vg1105850724:

Variant ID: vg1105850724 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5850724
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCTGTGGCGATAGGACTACTAAGGCACGACTGAAGACATCGAGCAACTCCGACTTCCTAAGACAAGCCAGAACATACCAACAAACCCACCAAGGAGC[G/A]
GGAATTACTAGGCGAAGCCTCCGACAAGGAAACAATATCAAGAATGTTGTCAATGTCCGTCCATAGCAATATACTAGGTTTTCATCTAAAGAAGAAGATG

Reverse complement sequence

CATCTTCTTCTTTAGATGAAAACCTAGTATATTGCTATGGACGGACATTGACAACATTCTTGATATTGTTTCCTTGTCGGAGGCTTCGCCTAGTAATTCC[C/T]
GCTCCTTGGTGGGTTTGTTGGTATGTTCTGGCTTGTCTTAGGAAGTCGGAGTTGCTCGATGTCTTCAGTCGTGCCTTAGTAGTCCTATCGCCACAGGTTG

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	45.90%	9.70%	1.10%	43.27%	NA
All Indica	2759	18.40%	10.70%	1.74%	69.16%	NA
All Japonica	1512	92.50%	2.20%	0.13%	5.16%	NA
Aus	269	48.30%	42.80%	0.74%	8.18%	NA
Indica I	595	7.70%	9.10%	0.67%	82.52%	NA
Indica II	465	9.00%	5.40%	3.23%	82.37%	NA
Indica III	913	26.50%	11.20%	1.53%	60.79%	NA
Indica Intermediate	786	22.60%	14.50%	1.91%	60.94%	NA
Temperate Japonica	767	91.80%	1.40%	0.26%	6.52%	NA
Tropical Japonica	504	97.40%	1.00%	0.00%	1.59%	NA
Japonica Intermediate	241	84.20%	7.50%	0.00%	8.30%	NA
VI/Aromatic	96	91.70%	5.20%	0.00%	3.12%	NA
Intermediate	90	51.10%	11.10%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105850724	G -> A	LOC_Os11g10670.1	downstream_gene_variant ; 1329.0bp to feature; MODIFIER	silent_mutation	Average:15.416; most accessible tissue: Callus, score: 79.62	N	N	N	N
vg1105850724	G -> A	LOC_Os11g10650-LOC_Os11g10670	intergenic_region ; MODIFIER	silent_mutation	Average:15.416; most accessible tissue: Callus, score: 79.62	N	N	N	N
vg1105850724	G -> DEL	N	N	silent_mutation	Average:15.416; most accessible tissue: Callus, score: 79.62	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105850724	NA	3.99E-06	mr1419	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
vg1105850724	3.36E-06	3.36E-06	mr1419	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
vg1105850724	NA	4.62E-07	mr1569	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
vg1105850724	NA	2.03E-06	mr1677	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
vg1105850724	NA	5.68E-07	mr1863	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
vg1105850724	6.54E-06	6.54E-06	mr1863	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