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Detailed information for vg0616722436:

Variant ID: vg0616722436 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16722436
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAGGGTGAGGAGCCAATTTTGCGGACCATTCGACACGTACGTTCGACACGTACGTCGTGTGCGCGCATCGCCTGCCAGGCCAGGCCAGGCGAGCGAGC[G/A]
CGCGCGTGTGTTCCCCCTCTTCTCTCCACCACACATGCTTCAAGTGGTAGGAGGACATCCTCCCTTTTAAGGAGGTCCCCCTCTCCTAGAATAAGTAAGG

Reverse complement sequence

CCTTACTTATTCTAGGAGAGGGGGACCTCCTTAAAAGGGAGGATGTCCTCCTACCACTTGAAGCATGTGTGGTGGAGAGAAGAGGGGGAACACACGCGCG[C/T]
GCTCGCTCGCCTGGCCTGGCCTGGCAGGCGATGCGCGCACACGACGTACGTGTCGAACGTACGTGTCGAATGGTCCGCAAAATTGGCTCCTCACCCTTAT

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	91.60%	8.00%	0.40%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	78.20%	21.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	96.70%	3.30%	0.00%	0.00%	NA
Tropical Japonica	504	59.70%	40.30%	0.00%	0.00%	NA
Japonica Intermediate	241	57.70%	41.90%	0.41%	0.00%	NA
VI/Aromatic	96	61.50%	22.90%	15.62%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0616722436	G -> A	LOC_Os06g29280.1	upstream_gene_variant ; 4959.0bp to feature; MODIFIER	silent_mutation	Average:39.978; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N
vg0616722436	G -> A	LOC_Os06g29290.1	downstream_gene_variant ; 2588.0bp to feature; MODIFIER	silent_mutation	Average:39.978; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N
vg0616722436	G -> A	LOC_Os06g29300.1	intron_variant ; MODIFIER	silent_mutation	Average:39.978; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616722436	NA	2.84E-07	mr1363_2	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
vg0616722436	NA	2.77E-07	mr1502_2	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
vg0616722436	NA	4.45E-11	mr1680_2	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