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Detailed information for vg0913073379:

Variant ID: vg0913073379 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13073379
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CACCTAGGCACGAGAGGGGACTGCCCGCTGCCTTGCGAGGAGTGGGGGTGAAACCTGAGGTGTGGTGTGCTTGGTTAGAGGGGGTTATGCGAAGGGTCCT[A/G]
TCACGGCCTCTTTCCGGTATGTCGTGGTGACATGTCGGCGCACGGAAACATGTCGTGGGGCTGTGTCTTGTGGGTACAGTTGTACACCTCTGATCAGAGT

Reverse complement sequence

ACTCTGATCAGAGGTGTACAACTGTACCCACAAGACACAGCCCCACGACATGTTTCCGTGCGCCGACATGTCACCACGACATACCGGAAAGAGGCCGTGA[T/C]
AGGACCCTTCGCATAACCCCCTCTAACCAAGCACACCACACCTCAGGTTTCACCCCCACTCCTCGCAAGGCAGCGGGCAGTCCCCTCTCGTGCCTAGGTG

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	25.30%	19.30%	47.29%	8.13%	NA
All Indica	2759	14.10%	24.70%	61.18%	0.04%	NA
All Japonica	1512	45.40%	1.70%	27.71%	25.20%	NA
Aus	269	6.70%	61.30%	31.97%	0.00%	NA
Indica I	595	15.30%	9.90%	74.79%	0.00%	NA
Indica II	465	7.30%	35.70%	56.99%	0.00%	NA
Indica III	913	16.60%	29.10%	54.22%	0.00%	NA
Indica Intermediate	786	14.10%	24.30%	61.45%	0.13%	NA
Temperate Japonica	767	77.60%	0.80%	6.78%	14.86%	NA
Tropical Japonica	504	8.10%	3.00%	61.31%	27.58%	NA
Japonica Intermediate	241	21.20%	1.70%	24.07%	53.11%	NA
VI/Aromatic	96	69.80%	24.00%	6.25%	0.00%	NA
Intermediate	90	41.10%	16.70%	40.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0913073379	A -> G	LOC_Os09g21590.1	upstream_gene_variant ; 2302.0bp to feature; MODIFIER	silent_mutation	Average:41.798; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0913073379	A -> G	LOC_Os09g21590-LOC_Os09g21600	intergenic_region ; MODIFIER	silent_mutation	Average:41.798; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0913073379	A -> DEL	N	N	silent_mutation	Average:41.798; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913073379	7.43E-06	7.43E-06	mr1591	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
vg0913073379	1.00E-06	1.00E-06	mr1663	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