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Detailed information for vg0912675777:

Variant ID: vg0912675777 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12675777
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAAAGTTTACATACCCGATTCAAATTTGAATTTGAATACAAATATTAATTTATAGACCCAAAGTTT[A/G]
TAAGTCAAAAATTTACATAACCGTTTCAATTCTGAATTTAAATTTAAATATTTATGATGTAGTAGGAAGAGAAAAAGGGAAGGAGGAAGGGGGGAGAGGA

Reverse complement sequence

TCCTCTCCCCCCTTCCTCCTTCCCTTTTTCTCTTCCTACTACATCATAAATATTTAAATTTAAATTCAGAATTGAAACGGTTATGTAAATTTTTGACTTA[T/C]
AAACTTTGGGTCTATAAATTAATATTTGTATTCAAATTCAAATTTGAATCGGGTATGTAAACTTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTG

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	96.10%	3.80%	0.08%	0.00%	NA
All Indica	2759	93.80%	6.10%	0.14%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.30%	9.10%	0.67%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	94.50%	5.50%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	5.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	95.60%	4.40%	0.00%	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
vg0912675777	A -> G	LOC_Os09g21020.1	upstream_gene_variant ; 1497.0bp to feature; MODIFIER	silent_mutation	Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0912675777	A -> G	LOC_Os09g21010.1	downstream_gene_variant ; 3753.0bp to feature; MODIFIER	silent_mutation	Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0912675777	A -> G	LOC_Os09g21010-LOC_Os09g21020	intergenic_region ; MODIFIER	silent_mutation	Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912675777	9.95E-06	6.22E-06	mr1150	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
vg0912675777	6.89E-07	7.89E-06	mr1247_2	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