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Detailed information for vg0609894917:

Variant ID: vg0609894917 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9894917
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TCATATATCGGCATATTTTAATCCAAAATATTAAGACAATAATCATGGCATGTACAATGTGGGGTGATCTAGTGATAAAATGTAACATAACCAGGAGCAT[G/A]
CTTAAAGTATAATAAGCATCATGAACATACAAAGAACGCAATAGAATTGCGACTAACAGGACAAACAGAGGTATCAAAGAATGAGTTAACAGTAGGAGAA

Reverse complement sequence

TTCTCCTACTGTTAACTCATTCTTTGATACCTCTGTTTGTCCTGTTAGTCGCAATTCTATTGCGTTCTTTGTATGTTCATGATGCTTATTATACTTTAAG[C/T]
ATGCTCCTGGTTATGTTACATTTTATCACTAGATCACCCCACATTGTACATGCCATGATTATTGTCTTAATATTTTGGATTAAAATATGCCGATATATGA

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	95.20%	4.10%	0.51%	0.15%	NA
All Indica	2759	92.10%	6.80%	0.87%	0.22%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.00%	2.50%	1.01%	0.50%	NA
Indica II	465	90.30%	8.20%	1.08%	0.43%	NA
Indica III	913	88.00%	11.70%	0.33%	0.00%	NA
Indica Intermediate	786	95.00%	3.60%	1.27%	0.13%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609894917	G -> A	LOC_Os06g17060.1	upstream_gene_variant ; 2920.0bp to feature; MODIFIER	silent_mutation	Average:42.435; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0609894917	G -> A	LOC_Os06g17070.1	intron_variant ; MODIFIER	silent_mutation	Average:42.435; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0609894917	G -> DEL	N	N	silent_mutation	Average:42.435; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609894917	8.46E-12	5.46E-14	mr1695	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
vg0609894917	9.40E-06	NA	mr1526_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
vg0609894917	2.37E-12	3.36E-18	mr1695_2	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