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Detailed information for vg1206433093:

Variant ID: vg1206433093 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6433093
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.33, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

AACAGACATAATGGTTGCACTCCCAGGGCTCACTACTACAAATATGATTTTTCCAAAGATCCAGGTATTATATTGATGGCAATGGGGTGTCCGATTTTCC[G/A]
TCAGGTGAAGATAATTATCGATCTGGAGAAAACTTGACACACACGATCTGCAAAATCCGAACCCTTCAATCGCAGCACTACGTCTTTTTTGGTTATCAAC

Reverse complement sequence

GTTGATAACCAAAAAAGACGTAGTGCTGCGATTGAAGGGTTCGGATTTTGCAGATCGTGTGTGTCAAGTTTTCTCCAGATCGATAATTATCTTCACCTGA[C/T]
GGAAAATCGGACACCCCATTGCCATCAATATAATACCTGGATCTTTGGAAAAATCATATTTGTAGTAGTGAGCCCTGGGAGTGCAACCATTATGTCTGTT

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	25.50%	15.90%	0.32%	58.32%	NA
All Indica	2759	36.90%	7.20%	0.40%	55.49%	NA
All Japonica	1512	5.80%	30.70%	0.20%	63.36%	NA
Aus	269	1.50%	21.90%	0.37%	76.21%	NA
Indica I	595	86.70%	4.20%	0.00%	9.08%	NA
Indica II	465	20.60%	18.10%	1.08%	60.22%	NA
Indica III	913	11.40%	2.70%	0.33%	85.54%	NA
Indica Intermediate	786	38.30%	8.40%	0.38%	52.93%	NA
Temperate Japonica	767	9.00%	40.00%	0.39%	50.59%	NA
Tropical Japonica	504	2.20%	10.50%	0.00%	87.30%	NA
Japonica Intermediate	241	2.90%	43.20%	0.00%	53.94%	NA
VI/Aromatic	96	69.80%	10.40%	0.00%	19.79%	NA
Intermediate	90	33.30%	18.90%	0.00%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206433093	G -> DEL	N	N	silent_mutation	Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756	N	N	N	N
vg1206433093	G -> A	LOC_Os12g11840.1	downstream_gene_variant ; 3301.0bp to feature; MODIFIER	silent_mutation	Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756	N	N	N	N
vg1206433093	G -> A	LOC_Os12g11840-LOC_Os12g11860	intergenic_region ; MODIFIER	silent_mutation	Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206433093	4.54E-06	NA	mr1177	Jap_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
vg1206433093	7.55E-07	7.55E-07	mr1381	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
vg1206433093	NA	2.41E-08	mr1030_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
vg1206433093	NA	6.94E-06	mr1184_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
vg1206433093	NA	5.11E-06	mr1278_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
vg1206433093	NA	2.84E-06	mr1329_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
vg1206433093	NA	1.85E-06	mr1369_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
vg1206433093	NA	2.27E-07	mr1524_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
vg1206433093	1.14E-06	NA	mr1549_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
vg1206433093	NA	5.48E-06	mr1652_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
vg1206433093	NA	6.51E-08	mr1683_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
vg1206433093	NA	1.37E-06	mr1687_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
vg1206433093	5.51E-06	1.12E-06	mr1923_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