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Detailed information for vg0906928402:

Variant ID: vg0906928402 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6928402
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AACCAAGAGCGAAACAAATTCCAAGATACTCCTTTGGCATACAAAGAGGACTACTAAAGATTACATAAGATTTTTCGGAGCTTTTGGGTATTCATTGTAG[C/G]
TAAGAGCCTAAGACCTCTCCCAACAATAAGCCAACACACAGCAGTGGAGCCAGTGTCTGGCCACCCAAGTCACTCGCCTGGGCTCATCGGCATGAAACAA

Reverse complement sequence

TTGTTTCATGCCGATGAGCCCAGGCGAGTGACTTGGGTGGCCAGACACTGGCTCCACTGCTGTGTGTTGGCTTATTGTTGGGAGAGGTCTTAGGCTCTTA[G/C]
CTACAATGAATACCCAAAAGCTCCGAAAAATCTTATGTAATCTTTAGTAGTCCTCTTTGTATGCCAAAGGAGTATCTTGGAATTTGTTTCGCTCTTGGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.50%	4.90%	0.34%	9.33%	NA
All Indica	2759	98.60%	0.70%	0.04%	0.65%	NA
All Japonica	1512	64.50%	13.60%	0.86%	21.03%	NA
Aus	269	74.00%	0.00%	0.00%	26.02%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	98.20%	0.40%	0.00%	1.31%	NA
Indica Intermediate	786	97.60%	1.70%	0.00%	0.76%	NA
Temperate Japonica	767	76.30%	5.60%	0.65%	17.47%	NA
Tropical Japonica	504	55.00%	15.50%	1.39%	28.17%	NA
Japonica Intermediate	241	46.90%	35.30%	0.41%	17.43%	NA
VI/Aromatic	96	66.70%	0.00%	2.08%	31.25%	NA
Intermediate	90	90.00%	4.40%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906928402	C -> G	LOC_Os09g12220.1	upstream_gene_variant ; 223.0bp to feature; MODIFIER	silent_mutation	Average:59.088; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0906928402	C -> G	LOC_Os09g12210-LOC_Os09g12220	intergenic_region ; MODIFIER	silent_mutation	Average:59.088; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0906928402	C -> DEL	N	N	silent_mutation	Average:59.088; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906928402	4.89E-07	4.89E-07	mr1323_2	Jap_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
vg0906928402	NA	9.06E-08	mr1695_2	Jap_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