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Detailed information for vg0906313973:

Variant ID: vg0906313973 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6313973
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TCGTCTTCCGTCGCCGACAGGTTATGCCGCCGCCAACTGGTTCTTTTATCTTCACAACTGCGCGTCTTCACTACCGGTTTGCTTCTGTTGCTGCCGACTC[G/A]
TGTTCACTTCATCACGGCTATGCAATTTTGTCACCATGGTGGAGCAACTTCATTTTTATTATCTTCGGCATCGGCAAACTCTATTGCCTCTACTTCACCA

Reverse complement sequence

TGGTGAAGTAGAGGCAATAGAGTTTGCCGATGCCGAAGATAATAAAAATGAAGTTGCTCCACCATGGTGACAAAATTGCATAGCCGTGATGAAGTGAACA[C/T]
GAGTCGGCAGCAACAGAAGCAAACCGGTAGTGAAGACGCGCAGTTGTGAAGATAAAAGAACCAGTTGGCGGCGGCATAACCTGTCGGCGACGGAAGACGA

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	62.60%	30.00%	0.36%	7.09%	NA
All Indica	2759	44.50%	50.40%	0.36%	4.71%	NA
All Japonica	1512	86.80%	0.50%	0.40%	12.37%	NA
Aus	269	93.70%	0.70%	0.37%	5.20%	NA
Indica I	595	26.60%	67.10%	0.67%	5.71%	NA
Indica II	465	69.20%	30.50%	0.00%	0.22%	NA
Indica III	913	37.90%	57.70%	0.22%	4.16%	NA
Indica Intermediate	786	51.10%	41.10%	0.51%	7.25%	NA
Temperate Japonica	767	94.50%	0.30%	0.13%	5.08%	NA
Tropical Japonica	504	86.50%	0.40%	0.60%	12.50%	NA
Japonica Intermediate	241	62.70%	1.20%	0.83%	35.27%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	18.90%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906313973	G -> DEL	N	N	silent_mutation	Average:37.28; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N
vg0906313973	G -> A	LOC_Os09g11360.1	upstream_gene_variant ; 2840.0bp to feature; MODIFIER	silent_mutation	Average:37.28; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N
vg0906313973	G -> A	LOC_Os09g11360-LOC_Os09g11370	intergenic_region ; MODIFIER	silent_mutation	Average:37.28; most accessible tissue: Minghui63 flag leaf, score: 55.068	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906313973	4.47E-06	NA	mr1478	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
vg0906313973	NA	1.15E-06	mr1160_2	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