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Detailed information for vg0609350915:

Variant ID: vg0609350915 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9350915
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATGAAAGACGGAAAAAAATCATTGGCTTATCAAATTCTCTATCGAGCCATGAAAAATTTTTTCAACAAAAATGTGAATTAGGAAGGATTGGTCGACG[A/G]
AATATGAATCGAAGACTGAATCTTGATATACCTCATAACAGCACCTTCTTGTTACCGCGAAATGCAATAGGCAATCGGCTAGATGGCACATCCAACCTGT

Reverse complement sequence

ACAGGTTGGATGTGCCATCTAGCCGATTGCCTATTGCATTTCGCGGTAACAAGAAGGTGCTGTTATGAGGTATATCAAGATTCAGTCTTCGATTCATATT[T/C]
CGTCGACCAATCCTTCCTAATTCACATTTTTGTTGAAAAAATTTTTCATGGCTCGATAGAGAATTTGATAAGCCAATGATTTTTTTCCGTCTTTCATAAT

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	59.40%	39.80%	0.38%	0.51%	NA
All Indica	2759	82.10%	16.70%	0.54%	0.58%	NA
All Japonica	1512	29.90%	69.60%	0.07%	0.40%	NA
Aus	269	14.90%	84.80%	0.00%	0.37%	NA
Indica I	595	85.70%	14.30%	0.00%	0.00%	NA
Indica II	465	82.20%	16.60%	0.00%	1.29%	NA
Indica III	913	80.10%	18.00%	1.64%	0.33%	NA
Indica Intermediate	786	81.80%	17.30%	0.00%	0.89%	NA
Temperate Japonica	767	54.50%	45.10%	0.13%	0.26%	NA
Tropical Japonica	504	2.00%	97.40%	0.00%	0.60%	NA
Japonica Intermediate	241	10.00%	89.60%	0.00%	0.41%	NA
VI/Aromatic	96	4.20%	94.80%	0.00%	1.04%	NA
Intermediate	90	47.80%	50.00%	2.22%	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
vg0609350915	A -> G	LOC_Os06g16380.1	upstream_gene_variant ; 336.0bp to feature; MODIFIER	silent_mutation	Average:43.316; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg0609350915	A -> G	LOC_Os06g16390.1	upstream_gene_variant ; 2798.0bp to feature; MODIFIER	silent_mutation	Average:43.316; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg0609350915	A -> G	LOC_Os06g16380-LOC_Os06g16390	intergenic_region ; MODIFIER	silent_mutation	Average:43.316; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg0609350915	A -> DEL	N	N	silent_mutation	Average:43.316; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609350915	2.54E-08	4.25E-08	mr1091_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
vg0609350915	5.44E-06	6.18E-06	mr1110_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