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Detailed information for vg0607346885:

Variant ID: vg0607346885 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7346885
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGTACAAATAATCAAGCCGAATATGATGCTTTATTATTCATCAAAAAGGCAGGGGGCATGCGTTTACACCTGAATTTGGCACCTAGGTTCAAAACAAG[G/A]
AAAATTGCCAAGATTTGAGAAAGTTGTCGGTTTCCTCTACTAGGCCGGTCTGACCGCCATATATGGGCCGGTCTAACCTGCAGCATTTGGCCGGTCGTAC

Reverse complement sequence

GTACGACCGGCCAAATGCTGCAGGTTAGACCGGCCCATATATGGCGGTCAGACCGGCCTAGTAGAGGAAACCGACAACTTTCTCAAATCTTGGCAATTTT[C/T]
CTTGTTTTGAACCTAGGTGCCAAATTCAGGTGTAAACGCATGCCCCCTGCCTTTTTGATGAATAATAAAGCATCATATTCGGCTTGATTATTTGTACAAA

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	43.40%	6.80%	6.41%	43.38%	NA
All Indica	2759	10.40%	9.60%	10.29%	69.74%	NA
All Japonica	1512	98.70%	0.50%	0.07%	0.66%	NA
Aus	269	71.40%	0.40%	0.37%	27.88%	NA
Indica I	595	19.50%	4.40%	14.79%	61.34%	NA
Indica II	465	5.20%	17.00%	9.03%	68.82%	NA
Indica III	913	5.40%	11.30%	6.90%	76.45%	NA
Indica Intermediate	786	12.30%	7.30%	11.58%	68.83%	NA
Temperate Japonica	767	99.30%	0.30%	0.13%	0.26%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	96.30%	2.10%	0.00%	1.66%	NA
VI/Aromatic	96	27.10%	38.50%	13.54%	20.83%	NA
Intermediate	90	60.00%	12.20%	4.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607346885	G -> A	LOC_Os06g13350.1	upstream_gene_variant ; 1972.0bp to feature; MODIFIER	silent_mutation	Average:46.979; most accessible tissue: Minghui63 flag leaf, score: 71.577	N	N	N	N
vg0607346885	G -> A	LOC_Os06g13360.1	intron_variant ; MODIFIER	silent_mutation	Average:46.979; most accessible tissue: Minghui63 flag leaf, score: 71.577	N	N	N	N
vg0607346885	G -> DEL	N	N	silent_mutation	Average:46.979; most accessible tissue: Minghui63 flag leaf, score: 71.577	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607346885	NA	9.35E-08	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
vg0607346885	9.16E-09	2.18E-61	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
vg0607346885	2.33E-07	5.08E-08	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
vg0607346885	6.97E-16	1.09E-99	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
vg0607346885	1.60E-14	5.54E-15	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