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Detailed information for vg0607815296:

Variant ID: vg0607815296 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7815296
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAAAAATGAATTTGTTTTTATTTTTTAAGGTAACTCCTATATAAAATGTTTTTTTTCATAAATACATCGTTTAGTAGTTTAAAAAAAATATGCTAACA[A/G]
AAAATAAGAAAGTAGGCAAACCGAACGCAGTTTAGAACGGACCATAAGATGAATAAGTTCAATATATGAGTTGGGTGAATACATTGGATAAACTCCAAAT

Reverse complement sequence

ATTTGGAGTTTATCCAATGTATTCACCCAACTCATATATTGAACTTATTCATCTTATGGTCCGTTCTAAACTGCGTTCGGTTTGCCTACTTTCTTATTTT[T/C]
TGTTAGCATATTTTTTTTAAACTACTAAACGATGTATTTATGAAAAAAAACATTTTATATAGGAGTTACCTTAAAAAATAAAAACAAATTCATTTTTTCA

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	57.20%	42.50%	0.06%	0.30%	NA
All Indica	2759	32.10%	67.40%	0.07%	0.43%	NA
All Japonica	1512	99.10%	0.80%	0.00%	0.07%	NA
Aus	269	84.80%	15.20%	0.00%	0.00%	NA
Indica I	595	13.30%	85.70%	0.17%	0.84%	NA
Indica II	465	72.50%	27.10%	0.00%	0.43%	NA
Indica III	913	19.30%	80.10%	0.11%	0.55%	NA
Indica Intermediate	786	37.40%	62.60%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	76.70%	21.10%	1.11%	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
vg0607815296	A -> G	LOC_Os06g14030-LOC_Os06g14040	intergenic_region ; MODIFIER	silent_mutation	Average:54.295; most accessible tissue: Callus, score: 75.345	N	N	N	N
vg0607815296	A -> DEL	N	N	silent_mutation	Average:54.295; most accessible tissue: Callus, score: 75.345	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607815296	NA	7.59E-15	mr1133_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
vg0607815296	NA	6.82E-07	mr1185_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
vg0607815296	NA	7.34E-08	mr1269_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
vg0607815296	NA	8.25E-07	mr1272_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
vg0607815296	NA	1.81E-06	mr1355_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
vg0607815296	NA	3.79E-08	mr1399_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
vg0607815296	NA	1.18E-07	mr1457_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
vg0607815296	NA	2.27E-07	mr1458_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
vg0607815296	NA	9.69E-09	mr1478_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
vg0607815296	NA	1.24E-07	mr1479_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
vg0607815296	NA	2.36E-07	mr1662_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
vg0607815296	NA	3.19E-08	mr1677_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
vg0607815296	NA	2.55E-14	mr1726_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
vg0607815296	NA	3.79E-09	mr1860_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
vg0607815296	NA	4.91E-14	mr1950_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