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Detailed information for vg0141089936:

Variant ID: vg0141089936 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41089936
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, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCCTCCGGCCAAAAGCAAAGCTAGAGAAAAAAATCCAAGTACTAAACCTCTAATAAGCGCACAACATTCCCAATCAGTGCCAGAGGCTGTTTATTAGA[G/A]
TTTCAACTTCTAAATTTAGCTTCAGTAGTTAGATCTATAGTAGAGTTGTGGAGCGGCCTAAACCCAACTCCAACTCTCTAGTTCAGTTTGTGAGAGAGCC

Reverse complement sequence

GGCTCTCTCACAAACTGAACTAGAGAGTTGGAGTTGGGTTTAGGCCGCTCCACAACTCTACTATAGATCTAACTACTGAAGCTAAATTTAGAAGTTGAAA[C/T]
TCTAATAAACAGCCTCTGGCACTGATTGGGAATGTTGTGCGCTTATTAGAGGTTTAGTACTTGGATTTTTTTCTCTAGCTTTGCTTTTGGCCGGAGGGGA

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	95.70%	3.90%	0.42%	0.00%	NA
All Indica	2759	93.10%	6.20%	0.72%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	84.40%	13.60%	2.02%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	90.10%	8.90%	1.02%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	97.80%	2.20%	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
vg0141089936	G -> A	LOC_Os01g70980.1	upstream_gene_variant ; 1768.0bp to feature; MODIFIER	silent_mutation	Average:57.535; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0141089936	G -> A	LOC_Os01g70990.1	upstream_gene_variant ; 367.0bp to feature; MODIFIER	silent_mutation	Average:57.535; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0141089936	G -> A	LOC_Os01g70980-LOC_Os01g70990	intergenic_region ; MODIFIER	silent_mutation	Average:57.535; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141089936	NA	2.91E-06	mr1038	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
vg0141089936	NA	1.67E-06	mr1038	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
vg0141089936	NA	5.44E-06	mr1177	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
vg0141089936	NA	2.81E-06	mr1376	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
vg0141089936	NA	3.17E-10	mr1389	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
vg0141089936	NA	3.32E-09	mr1389	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
vg0141089936	NA	2.81E-06	mr1431	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
vg0141089936	NA	6.03E-08	mr1611	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
vg0141089936	2.89E-06	1.07E-07	mr1636	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
vg0141089936	NA	2.00E-06	mr1706	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
vg0141089936	NA	6.10E-12	mr1038_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
vg0141089936	NA	3.50E-11	mr1038_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
vg0141089936	NA	7.87E-10	mr1389_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
vg0141089936	NA	1.99E-09	mr1389_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