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Detailed information for vg0411669826:

Variant ID: vg0411669826 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11669826
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.17, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGCGAACTAGAGCCAAGTGCTCCTCGATGTAGGGAGCCACCAATGAAGATTGTTGCAGAACCGTGAAATGGGCTTTACGGAATAAATTATTGTCTACC[A/G]
TCATTATTGCTTTCCTTCCGAGAGTCCCCTTTCCCCGTAGTCTCCCTTTATGGCGTGATTCAGGTATCCCGATTGGGCGATGCTTGCCTCTGGACGAGCG

Reverse complement sequence

CGCTCGTCCAGAGGCAAGCATCGCCCAATCGGGATACCTGAATCACGCCATAAAGGGAGACTACGGGGAAAGGGGACTCTCGGAAGGAAAGCAATAATGA[T/C]
GGTAGACAATAATTTATTCCGTAAAGCCCATTTCACGGTTCTGCAACAATCTTCATTGGTGGCTCCCTACATCGAGGAGCACTTGGCTCTAGTTCGCGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.10%	15.90%	34.28%	17.71%	NA
All Indica	2759	3.70%	16.10%	51.14%	29.14%	NA
All Japonica	1512	87.60%	11.60%	0.60%	0.26%	NA
Aus	269	18.60%	13.80%	60.22%	7.43%	NA
Indica I	595	1.00%	10.80%	52.27%	35.97%	NA
Indica II	465	3.90%	23.40%	48.39%	24.30%	NA
Indica III	913	5.10%	17.10%	52.68%	25.08%	NA
Indica Intermediate	786	3.80%	14.50%	50.13%	31.55%	NA
Temperate Japonica	767	92.20%	7.40%	0.13%	0.26%	NA
Tropical Japonica	504	90.10%	8.70%	0.79%	0.40%	NA
Japonica Intermediate	241	67.60%	30.70%	1.66%	0.00%	NA
VI/Aromatic	96	6.20%	81.20%	12.50%	0.00%	NA
Intermediate	90	42.20%	18.90%	28.89%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0411669826	A -> DEL	N	N	silent_mutation	Average:11.968; most accessible tissue: Callus, score: 23.012	N	N	N	N
vg0411669826	A -> G	LOC_Os04g20800.1	upstream_gene_variant ; 3570.0bp to feature; MODIFIER	silent_mutation	Average:11.968; most accessible tissue: Callus, score: 23.012	N	N	N	N
vg0411669826	A -> G	LOC_Os04g20790.1	intron_variant ; MODIFIER	silent_mutation	Average:11.968; most accessible tissue: Callus, score: 23.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411669826	4.85E-07	4.85E-07	mr1343	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
vg0411669826	NA	7.87E-06	mr1829	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
vg0411669826	NA	9.53E-08	mr1549_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
vg0411669826	NA	5.76E-06	mr1757_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