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Detailed information for vg0105903122:

Variant ID: vg0105903122 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5903122
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GTAAAAAAACCCAATGATAATCATGTTCGATTTTAAAATCTCAATGACAATAAAGAAAGTAGGCAGCGGGCGAGCCGTAGAGGAGTACAATGGCAAAGCC[G/A]
CTGATGGTTTGGCGAGACTTCTAGAAAGTAAAAATGAACCCAAACGATAATTATGTTTGATTTTTAAAATCTCAATGACAATAAAGAGAAGAAACAGTGG

Reverse complement sequence

CCACTGTTTCTTCTCTTTATTGTCATTGAGATTTTAAAAATCAAACATAATTATCGTTTGGGTTCATTTTTACTTTCTAGAAGTCTCGCCAAACCATCAG[C/T]
GGCTTTGCCATTGTACTCCTCTACGGCTCGCCCGCTGCCTACTTTCTTTATTGTCATTGAGATTTTAAAATCGAACATGATTATCATTGGGTTTTTTTAC

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	67.80%	29.70%	2.58%	0.00%	NA
All Indica	2759	65.70%	30.50%	3.73%	0.00%	NA
All Japonica	1512	79.40%	20.20%	0.46%	0.00%	NA
Aus	269	15.20%	81.00%	3.72%	0.00%	NA
Indica I	595	91.40%	6.90%	1.68%	0.00%	NA
Indica II	465	65.40%	32.30%	2.37%	0.00%	NA
Indica III	913	50.80%	45.30%	3.83%	0.00%	NA
Indica Intermediate	786	63.90%	30.20%	5.98%	0.00%	NA
Temperate Japonica	767	95.80%	4.00%	0.13%	0.00%	NA
Tropical Japonica	504	69.80%	29.40%	0.79%	0.00%	NA
Japonica Intermediate	241	46.90%	52.30%	0.83%	0.00%	NA
VI/Aromatic	96	83.30%	15.60%	1.04%	0.00%	NA
Intermediate	90	74.40%	24.40%	1.11%	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
vg0105903122	G -> A	LOC_Os01g11054.3	upstream_gene_variant ; 1908.0bp to feature; MODIFIER	silent_mutation	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0105903122	G -> A	LOC_Os01g11054.2	upstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0105903122	G -> A	LOC_Os01g11054.4	upstream_gene_variant ; 3957.0bp to feature; MODIFIER	silent_mutation	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0105903122	G -> A	LOC_Os01g11040.1	downstream_gene_variant ; 4898.0bp to feature; MODIFIER	silent_mutation	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N
vg0105903122	G -> A	LOC_Os01g11054.1	intron_variant ; MODIFIER	silent_mutation	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 50.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105903122	NA	3.03E-06	mr1104_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
vg0105903122	3.47E-06	3.47E-06	mr1145_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
vg0105903122	8.12E-06	1.34E-08	mr1155_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
vg0105903122	NA	8.52E-08	mr1180_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
vg0105903122	NA	2.15E-07	mr1183_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
vg0105903122	3.94E-06	3.95E-06	mr1264_2	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
vg0105903122	7.19E-06	NA	mr1408_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
vg0105903122	NA	8.41E-06	mr1437_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