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Detailed information for vg0607417912:

Variant ID: vg0607417912 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7417912
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCGACTCCGCATCCCATACGCACACAATACCTCTATCGTATGCCATTTGGAATTTTCACCAACCACGTGCATCAACTCTAGTCTTAGTATCCCGCAT[G/A]
ATATCTGACCATCACGGACATCGTCTTACCACCAATCCGACTCCCGGTCCATCACCACAAATACTCTCCCGAGGCATCGAGTCACCTACACATGAAACAA

Reverse complement sequence

TTGTTTCATGTGTAGGTGACTCGATGCCTCGGGAGAGTATTTGTGGTGATGGACCGGGAGTCGGATTGGTGGTAAGACGATGTCCGTGATGGTCAGATAT[C/T]
ATGCGGGATACTAAGACTAGAGTTGATGCACGTGGTTGGTGAAAATTCCAAATGGCATACGATAGAGGTATTGTGTGCGTATGGGATGCGGAGTCGAATT

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	52.50%	47.10%	0.34%	0.00%	NA
All Indica	2759	20.30%	79.20%	0.58%	0.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	22.70%	76.50%	0.84%	0.00%	NA
Indica II	465	5.20%	94.20%	0.65%	0.00%	NA
Indica III	913	23.80%	75.90%	0.33%	0.00%	NA
Indica Intermediate	786	23.30%	76.10%	0.64%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	0.00%	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
vg0607417912	G -> A	LOC_Os06g13470.1	intron_variant ; MODIFIER	silent_mutation	Average:17.153; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607417912	NA	2.24E-09	mr1929	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
vg0607417912	NA	1.02E-63	mr1970	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
vg0607417912	NA	4.24E-08	mr1970	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
vg0607417912	3.75E-08	1.74E-83	mr1973	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
vg0607417912	NA	4.16E-13	mr1973	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
vg0607417912	3.51E-09	7.07E-68	mr1970_2	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
vg0607417912	NA	3.07E-11	mr1970_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
vg0607417912	5.88E-12	6.80E-100	mr1973_2	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
vg0607417912	2.85E-08	2.75E-18	mr1973_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