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Detailed information for vg1207087706:

Variant ID: vg1207087706 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7087706
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAGCTAATAATTTAAATTTAAAAAAAAATATTATAAAGGAAAAAATTTAATCCTTAATGTCAATTTAAATCGGTAGATCCATAATATTAAACCGATGA[A/G]
CCCATTAAATCCACATATATGCACCACTGACTTTTGCCATTTGTGTGACAACCAAATAACAACGAAACAACATAGTAATAAATAATAACACACATATAAG

Reverse complement sequence

CTTATATGTGTGTTATTATTTATTACTATGTTGTTTCGTTGTTATTTGGTTGTCACACAAATGGCAAAAGTCAGTGGTGCATATATGTGGATTTAATGGG[T/C]
TCATCGGTTTAATATTATGGATCTACCGATTTAAATTGACATTAAGGATTAAATTTTTTCCTTTATAATATTTTTTTTTAAATTTAAATTATTAGCTAGA

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	74.60%	8.90%	1.69%	14.75%	NA
All Indica	2759	97.40%	0.50%	1.09%	1.01%	NA
All Japonica	1512	34.70%	23.70%	2.12%	39.48%	NA
Aus	269	68.80%	13.80%	5.20%	12.27%	NA
Indica I	595	99.00%	0.30%	0.00%	0.67%	NA
Indica II	465	93.50%	0.40%	4.52%	1.51%	NA
Indica III	913	98.80%	0.40%	0.33%	0.44%	NA
Indica Intermediate	786	96.70%	0.90%	0.76%	1.65%	NA
Temperate Japonica	767	40.70%	2.50%	1.43%	55.41%	NA
Tropical Japonica	504	16.90%	61.90%	2.98%	18.25%	NA
Japonica Intermediate	241	52.70%	11.60%	2.49%	33.20%	NA
VI/Aromatic	96	79.20%	0.00%	3.12%	17.71%	NA
Intermediate	90	62.20%	12.20%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207087706	A -> DEL	N	N	silent_mutation	Average:31.706; most accessible tissue: Minghui63 flower, score: 46.748	N	N	N	N
vg1207087706	A -> G	LOC_Os12g12840-LOC_Os12g12850	intergenic_region ; MODIFIER	silent_mutation	Average:31.706; most accessible tissue: Minghui63 flower, score: 46.748	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207087706	6.06E-06	NA	mr1236	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
vg1207087706	NA	2.33E-06	mr1304	Jap_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
vg1207087706	NA	1.31E-07	mr1345	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
vg1207087706	NA	2.55E-06	mr1382	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
vg1207087706	NA	8.19E-06	mr1382	Jap_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
vg1207087706	4.68E-06	9.42E-07	mr1417	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
vg1207087706	NA	1.74E-07	mr1551	Jap_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
vg1207087706	NA	9.21E-07	mr1583	Jap_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
vg1207087706	NA	2.58E-07	mr1696	Jap_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
vg1207087706	NA	1.18E-07	mr1697	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
vg1207087706	NA	7.09E-06	mr1876	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
vg1207087706	3.08E-06	NA	mr1906	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
vg1207087706	2.04E-07	NA	mr1960	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
vg1207087706	NA	9.22E-06	mr1815_2	Jap_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