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Detailed information for vg0411104386:

Variant ID: vg0411104386 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11104386
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

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

Flanking Sequence (100 bp) in Reference Genome:

AGCGGATTGATGAATTGCCGGCGCAGTTTTGTACTATAGCAGGAAATGGGGAAAATGGCGAGAGTCTCGGCGGGGAAGACGAAGAGACGTTTTATTTCAC[T/A]
TCGGTGTTATTAGCCTAAACACAGTACTTTAGCCCAATTTTATTTTCAGCGTGGCCCGTTGTGATCTCTAGGGACTTAGGCGCTTTTTGCTTTGGCAATT

Reverse complement sequence

AATTGCCAAAGCAAAAAGCGCCTAAGTCCCTAGAGATCACAACGGGCCACGCTGAAAATAAAATTGGGCTAAAGTACTGTGTTTAGGCTAATAACACCGA[A/T]
GTGAAATAAAACGTCTCTTCGTCTTCCCCGCCGAGACTCTCGCCATTTTCCCCATTTCCTGCTATAGTACAAAACTGCGCCGGCAATTCATCAATCCGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.40%	2.40%	7.55%	20.67%	NA
All Indica	2759	48.80%	3.80%	12.69%	34.69%	NA
All Japonica	1512	99.00%	0.10%	0.00%	0.86%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	24.40%	2.40%	15.29%	57.98%	NA
Indica II	465	66.00%	8.00%	5.38%	20.65%	NA
Indica III	913	59.60%	0.30%	9.75%	30.34%	NA
Indica Intermediate	786	44.50%	6.60%	18.45%	30.41%	NA
Temperate Japonica	767	98.20%	0.10%	0.00%	1.69%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	4.40%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0411104386	T -> DEL	N	N	silent_mutation	Average:33.173; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0411104386	T -> A	LOC_Os04g19910.1	upstream_gene_variant ; 211.0bp to feature; MODIFIER	silent_mutation	Average:33.173; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0411104386	T -> A	LOC_Os04g19920.1	upstream_gene_variant ; 1250.0bp to feature; MODIFIER	silent_mutation	Average:33.173; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0411104386	T -> A	LOC_Os04g19900.1	downstream_gene_variant ; 3438.0bp to feature; MODIFIER	silent_mutation	Average:33.173; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0411104386	T -> A	LOC_Os04g19910-LOC_Os04g19920	intergenic_region ; MODIFIER	silent_mutation	Average:33.173; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411104386	4.36E-06	4.36E-06	mr1782	Ind_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