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Detailed information for vg0906520037:

Variant ID: vg0906520037 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6520037
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGAGTGTGGAGCGATGTGCTTACCCCCTACGGTGTTAGAGTTTTTGTGTTAAAGTGGAGTTGGAGCTGTCATCGGGTTCAGCCGATGAGCTAGGCAAC[G/A]
ATAACACTCAACACTCTTGCTCTAGCTTCTTAGAGGTCCTGTACTTCTTGAGGGAGTCTTGGGCGACAGCCCTGCCTGGTCTTCTAGGATCGGTGACATC

Reverse complement sequence

GATGTCACCGATCCTAGAAGACCAGGCAGGGCTGTCGCCCAAGACTCCCTCAAGAAGTACAGGACCTCTAAGAAGCTAGAGCAAGAGTGTTGAGTGTTAT[C/T]
GTTGCCTAGCTCATCGGCTGAACCCGATGACAGCTCCAACTCCACTTTAACACAAAAACTCTAACACCGTAGGGGGTAAGCACATCGCTCCACACTCGGC

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	67.20%	5.50%	0.68%	26.68%	NA
All Indica	2759	52.30%	1.80%	0.94%	44.98%	NA
All Japonica	1512	87.80%	11.20%	0.40%	0.53%	NA
Aus	269	86.60%	13.40%	0.00%	0.00%	NA
Indica I	595	34.60%	0.00%	1.34%	64.03%	NA
Indica II	465	64.30%	6.70%	0.43%	28.60%	NA
Indica III	913	51.20%	0.40%	0.66%	47.75%	NA
Indica Intermediate	786	59.90%	1.80%	1.27%	37.02%	NA
Temperate Japonica	767	96.60%	3.10%	0.00%	0.26%	NA
Tropical Japonica	504	84.90%	12.70%	1.19%	1.19%	NA
Japonica Intermediate	241	66.00%	34.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	3.30%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906520037	G -> DEL	N	N	silent_mutation	Average:45.538; most accessible tissue: Minghui63 young leaf, score: 79.896	N	N	N	N
vg0906520037	G -> A	LOC_Os09g11690.1	downstream_gene_variant ; 3976.0bp to feature; MODIFIER	silent_mutation	Average:45.538; most accessible tissue: Minghui63 young leaf, score: 79.896	N	N	N	N
vg0906520037	G -> A	LOC_Os09g11680.1	intron_variant ; MODIFIER	silent_mutation	Average:45.538; most accessible tissue: Minghui63 young leaf, score: 79.896	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906520037	4.31E-06	NA	mr1693	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