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Detailed information for vg0607535749:

Variant ID: vg0607535749 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7535749
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, A: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TATTAATTTTGCTTGTCTCGATCATTTTGGACCAGCTTCGCACAGACTAGTCAAGTTAATGCACTGAATTGACCAATTTATAAGTTTTCTTTACCTATTT[G/A]
TACCCACTATACAAGTTCAAGCATAATTTACTCTATATTTTAATACTACTAAAAGGGGTTGTAATATTTTTTTAATATAATTAAGTTCATTTTAATACTG

Reverse complement sequence

CAGTATTAAAATGAACTTAATTATATTAAAAAAATATTACAACCCCTTTTAGTAGTATTAAAATATAGAGTAAATTATGCTTGAACTTGTATAGTGGGTA[C/T]
AAATAGGTAAAGAAAACTTATAAATTGGTCAATTCAGTGCATTAACTTGACTAGTCTGTGCGAAGCTGGTCCAAAATGATCGAGACAAGCAAAATTAATA

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	89.40%	9.10%	1.52%	0.00%	NA
All Indica	2759	82.70%	14.60%	2.61%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	64.40%	27.20%	8.40%	0.00%	NA
Indica II	465	97.20%	1.50%	1.29%	0.00%	NA
Indica III	913	86.10%	13.80%	0.11%	0.00%	NA
Indica Intermediate	786	84.20%	13.90%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	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	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0607535749	G -> A	LOC_Os06g13600.1	downstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:67.928; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N
vg0607535749	G -> A	LOC_Os06g13600-LOC_Os06g13610	intergenic_region ; MODIFIER	silent_mutation	Average:67.928; most accessible tissue: Zhenshan97 root, score: 85.305	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607535749	NA	1.11E-09	mr1201	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
vg0607535749	NA	1.29E-08	mr1201	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
vg0607535749	NA	1.37E-06	mr1219	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
vg0607535749	NA	6.51E-07	mr1219	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
vg0607535749	NA	2.47E-09	mr1274	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
vg0607535749	NA	3.05E-07	mr1274	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
vg0607535749	4.26E-06	6.28E-11	mr1201_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
vg0607535749	NA	2.30E-09	mr1201_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
vg0607535749	NA	5.63E-07	mr1219_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
vg0607535749	NA	1.13E-07	mr1219_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
vg0607535749	1.85E-06	5.82E-12	mr1274_2	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
vg0607535749	2.05E-06	3.85E-11	mr1274_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
vg0607535749	2.64E-06	7.16E-07	mr1973_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